The transcriptional coactivator Eya1 exerts transcriptional repressive activity by interacting with REST corepressors and DNA recognition sequences to maintain nephron progenitor identity

To investigate the transcriptional network regulated by Eya1, the author perform Eya1 ChIP-seq. 80 kidneys from E13.5 Eya1(HA-FLAG) knockin mice were used. The kidneys were homogenized, lysed, and sonicated and purified. After washing, FLAG peptide was usedfor elution. Then generate sequence libraries and sequenced on Illumina NextSeq500.

In [2]:
mkdir -p /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/
In [2]:
cd /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/

To download the sra and raw fastq files

In [6]:
prefetch SRR19193869 -O /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq
2022-12-01T23:23:51 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-12-01T23:23:51 prefetch.3.0.0: 1) Downloading 'SRR19193869'...
2022-12-01T23:23:51 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-12-01T23:23:51 prefetch.3.0.0:  Downloading via HTTPS...
2022-12-01T23:24:17 prefetch.3.0.0:  HTTPS download succeed
2022-12-01T23:24:19 prefetch.3.0.0:  'SRR19193869' is valid
2022-12-01T23:24:19 prefetch.3.0.0: 1) 'SRR19193869' was downloaded successfully
2022-12-01T23:24:19 prefetch.3.0.0: 'SRR19193869' has 0 unresolved dependencies
In [13]:
prefetch SRR19193868 -O /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq
2022-12-01T23:36:39 prefetch.3.0.0: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2022-12-01T23:36:40 prefetch.3.0.0: 1) Downloading 'SRR19193868'...
2022-12-01T23:36:40 prefetch.3.0.0: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2022-12-01T23:36:40 prefetch.3.0.0:  Downloading via HTTPS...
2022-12-01T23:37:32 prefetch.3.0.0:  HTTPS download succeed
2022-12-01T23:37:34 prefetch.3.0.0:  'SRR19193868' is valid
2022-12-01T23:37:34 prefetch.3.0.0: 1) 'SRR19193868' was downloaded successfully
2022-12-01T23:37:34 prefetch.3.0.0: 'SRR19193868' has 0 unresolved dependencies
In [7]:
fastq-dump --split-files /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra
Rejected 42853510 READS because READLEN < 1
Read 42853510 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra
Written 42853510 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193869/SRR19193869.sra

Rejected 42853510 READS because READLEN < 1 => length of second reads is 0 (Single-end) => is ok to use this fastq file image.png

In [14]:
fastq-dump --split-files /mnt/storage/$USER/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra
Rejected 44976090 READS because READLEN < 1
Read 44976090 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra
Written 44976090 spots for /mnt/storage/r0823712/jupyternotebooks/assignment2/ChIP-seq/SRR19193868/SRR19193868.sra

image.png

In [17]:
ls -lt *.fastq
-rw-r--r-- 1 r0823712 domain users 8231156148 Dec  2 00:41 SRR19193868.fastq
-rw-r--r-- 1 r0823712 domain users 7840601428 Dec  2 00:27 SRR19193869.fastq

Check read quality

In [12]:
fastqc SRR19193869.fastq
Started analysis of SRR19193869.fastq
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Analysis complete for SRR19193869.fastq
In [16]:
fastqc SRR19193868.fastq
Started analysis of SRR19193868.fastq
Approx 5% complete for SRR19193868.fastq
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Analysis complete for SRR19193868.fastq
In [18]:
ls -lt | head
total 15697148
-rw-r--r-- 1 r0823712 domain users     663787 Dec  2 00:44 SRR19193868_fastqc.html
-rw-r--r-- 1 r0823712 domain users     381822 Dec  2 00:44 SRR19193868_fastqc.zip
-rw-r--r-- 1 r0823712 domain users 8231156148 Dec  2 00:41 SRR19193868.fastq
drwxr-xr-x 2 r0823712 domain users         37 Dec  2 00:37 SRR19193868
-rw-r--r-- 1 r0823712 domain users     674349 Dec  2 00:35 SRR19193869_fastqc.html
-rw-r--r-- 1 r0823712 domain users     386461 Dec  2 00:35 SRR19193869_fastqc.zip
-rw-r--r-- 1 r0823712 domain users 7840601428 Dec  2 00:27 SRR19193869.fastq
drwxr-xr-x 2 r0823712 domain users         37 Dec  2 00:24 SRR19193869
In [19]:
wc SRR19193869.fastq
wc SRR19193868.fastq
 171414040  342828080 7840601428 SRR19193869.fastq
 179904360  359808720 8231156148 SRR19193868.fastq

image.png quality is ok

Alignment of Eya1 ChIP-seq reads

In [22]:
bowtie2 -x /mnt/storage/data/resources/genomes/mm10/bowtie2/mm10 SRR19193868.fastq -S ChIP_Eya1.sam
44976090 reads; of these:
  44976090 (100.00%) were unpaired; of these:
    1246965 (2.77%) aligned 0 times
    32314194 (71.85%) aligned exactly 1 time
    11414931 (25.38%) aligned >1 times
97.23% overall alignment rate
In [23]:
#Check a couple of lines in the SAM file
head -500 ChIP_Eya1.sam | tail -5
SRR19193868.428	16	chr19	10025990	42	50M	*	0	0	TCTATTATGCCTGGACTATTTGTAGACTCTTCCTGCCTGCTGAGGCCTGN	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDD<#	AS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:49G0	YT:Z:UU
SRR19193868.429	0	chr12	52150953	42	50M	*	0	0	CACCTCCACTGTCACCTCCACTGCCACCTCCACTGCCACTGCCACCTCCA	DDDDBHHHIGEHHCHHIIIIIECHC1GEHHHF?@GHFHHHIIGHHIIHCC	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
SRR19193868.430	16	chr10	50503366	42	50M	*	0	0	GCAATGAAAAGAGTGTGTACAATTACATCCTAGAGTCAGTTCATCTAGTN	IIIIIIIIIIIIIIIIIIIIIHIIHIIIIIIIHGIIIIIIIIIIIDD<<#	AS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:49C0	YT:Z:UU
SRR19193868.431	4	*	0	0	*	*	0	0	NCCTTCTGTGGGCATTTCCCATTTTTCAGGTTTTTTAGTGATTTCGTAGA	#<<DDIIIIIIIIIIIIIIIIIIIIHIIIIHGHIIIIIIIIIIIIIIIIH	YT:Z:UU
SRR19193868.432	16	chr15	58867315	42	50M	*	0	0	TGGACCCCAGCAGTCAGTAGACCAAGAGTGAAGCTCAACTAGGGGCTGTN	IIHIIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIDDD<#	AS:i:-1	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:49C0	YT:Z:UU
In [24]:
#Convert the SAM file to BAM format (binary)
samtools view -S -b ChIP_Eya1.sam > ChIP_Eya1.bam
In [25]:
samtools view -c ChIP_Eya1.bam
#-c: count
44976090
In [26]:
# Number of mapped reads.(only one position)
samtools view -c -F 260 ChIP_Eya1.bam
#unmapped reads and not primary alignment would be removed
43729125
In [27]:
samtools sort -O bam -o ChIP_Eya1.sorted.bam ChIP_Eya1.bam
[bam_sort_core] merging from 11 files and 1 in-memory blocks...
In [30]:
samtools index ChIP_Eya1.sorted.bam
In [29]:
ls
ChIP_Eya1.bam             SRR19193868              SRR19193869
ChIP_Eya1.sam             SRR19193868.fastq        SRR19193869.fastq
ChIP_Eya1.sorted.bam      SRR19193868_fastqc.html  SRR19193869_fastqc.html
ChIP_Eya1.sorted.bam.bai  SRR19193868_fastqc.zip   SRR19193869_fastqc.zip

Alignment of the control data ("input")

In [20]:
bowtie2 -x /mnt/storage/data/resources/genomes/mm10/bowtie2/mm10 SRR19193869.fastq -S ChIP_input.sam
#-x: index
42853510 reads; of these:
  42853510 (100.00%) were unpaired; of these:
    1174124 (2.74%) aligned 0 times
    31783035 (74.17%) aligned exactly 1 time
    9896351 (23.09%) aligned >1 times
97.26% overall alignment rate
In [30]:
samtools view -S -b ChIP_input.sam > ChIP_input.bam
In [31]:
samtools sort -O bam -o ChIP_input.sorted.bam ChIP_input.bam
[bam_sort_core] merging from 10 files and 1 in-memory blocks...
In [29]:
samtools index ChIP_input.sorted.bam

BAM file in IGV

REST is a target gene of Eya1, located on chr5. A peak near 5' UTR of the two REST isoforms.

image.png

Genome-wide coverage plots

In [33]:
# generate a bigwig file that contains only the coverage of the reads
bamCoverage -b ChIP_Eya1.sorted.bam --normalizeUsing RPGC --effectiveGenomeSize 2652783500 -o ChIP_Eya1.bw -bs 5
#RPGC = reads per       genomic content (1x normalization); Mapped reads are considered after blacklist filtering (if applied).
#-bs: per how many bins I want to calculated in my bigwig
normalization: 1x (effective genome size 2652783500)
bamFilesList: ['ChIP_Eya1.sorted.bam']
binLength: 5
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 5
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000

image.png

Peak calling

Another example of a target gene, Zfx, located on X chromosome. Peaks in the intron and 3'UTR of the Zfx isoforms. image.png

Peak calling with MACS2

MACS can distinguish true, bona fide peaks, from artifacts.

In [14]:
macs2 callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05
#-t: real ChIP data
#-c: control = input
#-n: output file name
#-g: genome size
#-q: threshold for the peaks (less strengen => more peaks)
#     If q=0.05, get many peaks => still can do motif analysis on the top peaks based on fold change or q-value
INFO  @ Fri, 02 Dec 2022 23:23:17: 
# Command line: callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05
# ARGUMENTS LIST:
# name = Eya1
# format = AUTO
# ChIP-seq file = ['ChIP_Eya1.sorted.bam']
# control file = ['ChIP_input.sorted.bam']
# effective genome size = 2.65e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Paired-End mode is off
 
INFO  @ Fri, 02 Dec 2022 23:23:17: #1 read tag files... 
INFO  @ Fri, 02 Dec 2022 23:23:17: #1 read treatment tags... 
INFO  @ Fri, 02 Dec 2022 23:23:17: Detected format is: BAM 
INFO  @ Fri, 02 Dec 2022 23:23:17: * Input file is gzipped. 
INFO  @ Fri, 02 Dec 2022 23:23:19:  1000000 
INFO  @ Fri, 02 Dec 2022 23:23:21:  2000000 
INFO  @ Fri, 02 Dec 2022 23:23:24:  3000000 
INFO  @ Fri, 02 Dec 2022 23:23:26:  4000000 
INFO  @ Fri, 02 Dec 2022 23:23:28:  5000000 
INFO  @ Fri, 02 Dec 2022 23:23:30:  6000000 
INFO  @ Fri, 02 Dec 2022 23:23:32:  7000000 
INFO  @ Fri, 02 Dec 2022 23:23:34:  8000000 
INFO  @ Fri, 02 Dec 2022 23:23:36:  9000000 
INFO  @ Fri, 02 Dec 2022 23:23:38:  10000000 
INFO  @ Fri, 02 Dec 2022 23:23:41:  11000000 
INFO  @ Fri, 02 Dec 2022 23:23:43:  12000000 
INFO  @ Fri, 02 Dec 2022 23:23:45:  13000000 
INFO  @ Fri, 02 Dec 2022 23:23:47:  14000000 
INFO  @ Fri, 02 Dec 2022 23:23:49:  15000000 
INFO  @ Fri, 02 Dec 2022 23:23:51:  16000000 
INFO  @ Fri, 02 Dec 2022 23:23:53:  17000000 
INFO  @ Fri, 02 Dec 2022 23:23:56:  18000000 
INFO  @ Fri, 02 Dec 2022 23:23:58:  19000000 
INFO  @ Fri, 02 Dec 2022 23:24:00:  20000000 
INFO  @ Fri, 02 Dec 2022 23:24:02:  21000000 
INFO  @ Fri, 02 Dec 2022 23:24:04:  22000000 
INFO  @ Fri, 02 Dec 2022 23:24:06:  23000000 
INFO  @ Fri, 02 Dec 2022 23:24:08:  24000000 
INFO  @ Fri, 02 Dec 2022 23:24:10:  25000000 
INFO  @ Fri, 02 Dec 2022 23:24:13:  26000000 
INFO  @ Fri, 02 Dec 2022 23:24:15:  27000000 
INFO  @ Fri, 02 Dec 2022 23:24:17:  28000000 
INFO  @ Fri, 02 Dec 2022 23:24:19:  29000000 
INFO  @ Fri, 02 Dec 2022 23:24:21:  30000000 
INFO  @ Fri, 02 Dec 2022 23:24:23:  31000000 
INFO  @ Fri, 02 Dec 2022 23:24:26:  32000000 
INFO  @ Fri, 02 Dec 2022 23:24:28:  33000000 
INFO  @ Fri, 02 Dec 2022 23:24:30:  34000000 
INFO  @ Fri, 02 Dec 2022 23:24:32:  35000000 
INFO  @ Fri, 02 Dec 2022 23:24:34:  36000000 
INFO  @ Fri, 02 Dec 2022 23:24:36:  37000000 
INFO  @ Fri, 02 Dec 2022 23:24:38:  38000000 
INFO  @ Fri, 02 Dec 2022 23:24:41:  39000000 
INFO  @ Fri, 02 Dec 2022 23:24:43:  40000000 
INFO  @ Fri, 02 Dec 2022 23:24:45:  41000000 
INFO  @ Fri, 02 Dec 2022 23:24:47:  42000000 
INFO  @ Fri, 02 Dec 2022 23:24:49:  43000000 
INFO  @ Fri, 02 Dec 2022 23:24:51:  44000000 
INFO  @ Fri, 02 Dec 2022 23:24:53: #1.2 read input tags... 
INFO  @ Fri, 02 Dec 2022 23:24:53: Detected format is: BAM 
INFO  @ Fri, 02 Dec 2022 23:24:53: * Input file is gzipped. 
INFO  @ Fri, 02 Dec 2022 23:24:55:  1000000 
INFO  @ Fri, 02 Dec 2022 23:24:57:  2000000 
INFO  @ Fri, 02 Dec 2022 23:24:59:  3000000 
INFO  @ Fri, 02 Dec 2022 23:25:01:  4000000 
INFO  @ Fri, 02 Dec 2022 23:25:03:  5000000 
INFO  @ Fri, 02 Dec 2022 23:25:05:  6000000 
INFO  @ Fri, 02 Dec 2022 23:25:07:  7000000 
INFO  @ Fri, 02 Dec 2022 23:25:09:  8000000 
INFO  @ Fri, 02 Dec 2022 23:25:11:  9000000 
INFO  @ Fri, 02 Dec 2022 23:25:14:  10000000 
INFO  @ Fri, 02 Dec 2022 23:25:16:  11000000 
INFO  @ Fri, 02 Dec 2022 23:25:18:  12000000 
INFO  @ Fri, 02 Dec 2022 23:25:20:  13000000 
INFO  @ Fri, 02 Dec 2022 23:25:22:  14000000 
INFO  @ Fri, 02 Dec 2022 23:25:24:  15000000 
INFO  @ Fri, 02 Dec 2022 23:25:26:  16000000 
INFO  @ Fri, 02 Dec 2022 23:25:28:  17000000 
INFO  @ Fri, 02 Dec 2022 23:25:30:  18000000 
INFO  @ Fri, 02 Dec 2022 23:25:32:  19000000 
INFO  @ Fri, 02 Dec 2022 23:25:34:  20000000 
INFO  @ Fri, 02 Dec 2022 23:25:37:  21000000 
INFO  @ Fri, 02 Dec 2022 23:25:39:  22000000 
INFO  @ Fri, 02 Dec 2022 23:25:41:  23000000 
INFO  @ Fri, 02 Dec 2022 23:25:43:  24000000 
INFO  @ Fri, 02 Dec 2022 23:25:45:  25000000 
INFO  @ Fri, 02 Dec 2022 23:25:47:  26000000 
INFO  @ Fri, 02 Dec 2022 23:25:49:  27000000 
INFO  @ Fri, 02 Dec 2022 23:25:51:  28000000 
INFO  @ Fri, 02 Dec 2022 23:25:53:  29000000 
INFO  @ Fri, 02 Dec 2022 23:25:55:  30000000 
INFO  @ Fri, 02 Dec 2022 23:25:57:  31000000 
INFO  @ Fri, 02 Dec 2022 23:25:59:  32000000 
INFO  @ Fri, 02 Dec 2022 23:26:01:  33000000 
INFO  @ Fri, 02 Dec 2022 23:26:03:  34000000 
INFO  @ Fri, 02 Dec 2022 23:26:06:  35000000 
INFO  @ Fri, 02 Dec 2022 23:26:08:  36000000 
INFO  @ Fri, 02 Dec 2022 23:26:10:  37000000 
INFO  @ Fri, 02 Dec 2022 23:26:12:  38000000 
INFO  @ Fri, 02 Dec 2022 23:26:14:  39000000 
INFO  @ Fri, 02 Dec 2022 23:26:16:  40000000 
INFO  @ Fri, 02 Dec 2022 23:26:18:  41000000 
INFO  @ Fri, 02 Dec 2022 23:26:20:  42000000 
INFO  @ Fri, 02 Dec 2022 23:26:21: #1 tag size is determined as 50 bps 
INFO  @ Fri, 02 Dec 2022 23:26:21: #1 tag size = 50.0 
INFO  @ Fri, 02 Dec 2022 23:26:21: #1  total tags in treatment: 43729125 
INFO  @ Fri, 02 Dec 2022 23:26:21: #1 user defined the maximum tags... 
INFO  @ Fri, 02 Dec 2022 23:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Fri, 02 Dec 2022 23:26:22: #1  tags after filtering in treatment: 40711860 
INFO  @ Fri, 02 Dec 2022 23:26:22: #1  Redundant rate of treatment: 0.07 
INFO  @ Fri, 02 Dec 2022 23:26:22: #1  total tags in control: 41679386 
INFO  @ Fri, 02 Dec 2022 23:26:22: #1 user defined the maximum tags... 
INFO  @ Fri, 02 Dec 2022 23:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Fri, 02 Dec 2022 23:26:23: #1  tags after filtering in control: 39821414 
INFO  @ Fri, 02 Dec 2022 23:26:23: #1  Redundant rate of control: 0.04 
INFO  @ Fri, 02 Dec 2022 23:26:23: #1 finished! 
INFO  @ Fri, 02 Dec 2022 23:26:23: #2 Build Peak Model... 
INFO  @ Fri, 02 Dec 2022 23:26:23: #2 looking for paired plus/minus strand peaks... 
INFO  @ Fri, 02 Dec 2022 23:26:26: #2 number of paired peaks: 4574 
INFO  @ Fri, 02 Dec 2022 23:26:26: start model_add_line... 
INFO  @ Fri, 02 Dec 2022 23:26:27: start X-correlation... 
INFO  @ Fri, 02 Dec 2022 23:26:27: end of X-cor 
INFO  @ Fri, 02 Dec 2022 23:26:27: #2 finished! 
INFO  @ Fri, 02 Dec 2022 23:26:27: #2 predicted fragment length is 73 bps 
INFO  @ Fri, 02 Dec 2022 23:26:27: #2 alternative fragment length(s) may be 73 bps 
INFO  @ Fri, 02 Dec 2022 23:26:27: #2.2 Generate R script for model : Eya1_model.r 
WARNING @ Fri, 02 Dec 2022 23:26:27: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! 
WARNING @ Fri, 02 Dec 2022 23:26:27: #2 You may need to consider one of the other alternative d(s): 73 
WARNING @ Fri, 02 Dec 2022 23:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. 
INFO  @ Fri, 02 Dec 2022 23:26:27: #3 Call peaks... 
INFO  @ Fri, 02 Dec 2022 23:26:27: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 02 Dec 2022 23:29:25: #3 Call peaks for each chromosome... 
INFO  @ Sat, 03 Dec 2022 02:10:30: #4 Write output xls file... Eya1_peaks.xls 
INFO  @ Sat, 03 Dec 2022 02:10:30: #4 Write peak in narrowPeak format file... Eya1_peaks.narrowPeak 
INFO  @ Sat, 03 Dec 2022 02:10:30: #4 Write summits bed file... Eya1_summits.bed 
INFO  @ Sat, 03 Dec 2022 02:10:30: Done! 

The uppe result show:\ WARNING Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem!

Maybe bad antibody or bad library prepareation cause poor ChIP quality.

In [3]:
macs2 callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05 --nomodel --extsize 73
#-t: real ChIP data
#-c: control = input
#-n: output file name
#-g: genome size
#-q: threshold for the peaks (less strengen => more peaks)
#     If q=0.05, get many peaks => still can do motif analysis on the top peaks based on fold change or q-value
INFO  @ Fri, 02 Dec 2022 19:45:14: 
# Command line: callpeak -t ChIP_Eya1.sorted.bam -c ChIP_input.sorted.bam -n Eya1 -g 2652783500 -q 0.05 --nomodel --extsize 73
# ARGUMENTS LIST:
# name = Eya1
# format = AUTO
# ChIP-seq file = ['ChIP_Eya1.sorted.bam']
# control file = ['ChIP_input.sorted.bam']
# effective genome size = 2.65e+09
# band width = 300
# model fold = [5, 50]
# qvalue cutoff = 5.00e-02
# The maximum gap between significant sites is assigned as the read length/tag size.
# The minimum length of peaks is assigned as the predicted fragment length "d".
# Larger dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps
# Broad region calling is off
# Paired-End mode is off
 
INFO  @ Fri, 02 Dec 2022 19:45:14: #1 read tag files... 
INFO  @ Fri, 02 Dec 2022 19:45:14: #1 read treatment tags... 
INFO  @ Fri, 02 Dec 2022 19:45:14: Detected format is: BAM 
INFO  @ Fri, 02 Dec 2022 19:45:14: * Input file is gzipped. 
INFO  @ Fri, 02 Dec 2022 19:45:17:  1000000 
INFO  @ Fri, 02 Dec 2022 19:45:19:  2000000 
INFO  @ Fri, 02 Dec 2022 19:45:21:  3000000 
INFO  @ Fri, 02 Dec 2022 19:45:23:  4000000 
INFO  @ Fri, 02 Dec 2022 19:45:25:  5000000 
INFO  @ Fri, 02 Dec 2022 19:45:27:  6000000 
INFO  @ Fri, 02 Dec 2022 19:45:29:  7000000 
INFO  @ Fri, 02 Dec 2022 19:45:31:  8000000 
INFO  @ Fri, 02 Dec 2022 19:45:33:  9000000 
INFO  @ Fri, 02 Dec 2022 19:45:36:  10000000 
INFO  @ Fri, 02 Dec 2022 19:45:38:  11000000 
INFO  @ Fri, 02 Dec 2022 19:45:40:  12000000 
INFO  @ Fri, 02 Dec 2022 19:45:42:  13000000 
INFO  @ Fri, 02 Dec 2022 19:45:44:  14000000 
INFO  @ Fri, 02 Dec 2022 19:45:46:  15000000 
INFO  @ Fri, 02 Dec 2022 19:45:48:  16000000 
INFO  @ Fri, 02 Dec 2022 19:45:50:  17000000 
INFO  @ Fri, 02 Dec 2022 19:45:52:  18000000 
INFO  @ Fri, 02 Dec 2022 19:45:55:  19000000 
INFO  @ Fri, 02 Dec 2022 19:45:57:  20000000 
INFO  @ Fri, 02 Dec 2022 19:45:59:  21000000 
INFO  @ Fri, 02 Dec 2022 19:46:01:  22000000 
INFO  @ Fri, 02 Dec 2022 19:46:03:  23000000 
INFO  @ Fri, 02 Dec 2022 19:46:05:  24000000 
INFO  @ Fri, 02 Dec 2022 19:46:07:  25000000 
INFO  @ Fri, 02 Dec 2022 19:46:09:  26000000 
INFO  @ Fri, 02 Dec 2022 19:46:11:  27000000 
INFO  @ Fri, 02 Dec 2022 19:46:13:  28000000 
INFO  @ Fri, 02 Dec 2022 19:46:16:  29000000 
INFO  @ Fri, 02 Dec 2022 19:46:18:  30000000 
INFO  @ Fri, 02 Dec 2022 19:46:20:  31000000 
INFO  @ Fri, 02 Dec 2022 19:46:22:  32000000 
INFO  @ Fri, 02 Dec 2022 19:46:24:  33000000 
INFO  @ Fri, 02 Dec 2022 19:46:26:  34000000 
INFO  @ Fri, 02 Dec 2022 19:46:28:  35000000 
INFO  @ Fri, 02 Dec 2022 19:46:30:  36000000 
INFO  @ Fri, 02 Dec 2022 19:46:32:  37000000 
INFO  @ Fri, 02 Dec 2022 19:46:34:  38000000 
INFO  @ Fri, 02 Dec 2022 19:46:36:  39000000 
INFO  @ Fri, 02 Dec 2022 19:46:38:  40000000 
INFO  @ Fri, 02 Dec 2022 19:46:41:  41000000 
INFO  @ Fri, 02 Dec 2022 19:46:43:  42000000 
INFO  @ Fri, 02 Dec 2022 19:46:45:  43000000 
INFO  @ Fri, 02 Dec 2022 19:46:47:  44000000 
INFO  @ Fri, 02 Dec 2022 19:46:48: #1.2 read input tags... 
INFO  @ Fri, 02 Dec 2022 19:46:48: Detected format is: BAM 
INFO  @ Fri, 02 Dec 2022 19:46:48: * Input file is gzipped. 
INFO  @ Fri, 02 Dec 2022 19:46:50:  1000000 
INFO  @ Fri, 02 Dec 2022 19:46:53:  2000000 
INFO  @ Fri, 02 Dec 2022 19:46:55:  3000000 
INFO  @ Fri, 02 Dec 2022 19:46:57:  4000000 
INFO  @ Fri, 02 Dec 2022 19:46:59:  5000000 
INFO  @ Fri, 02 Dec 2022 19:47:01:  6000000 
INFO  @ Fri, 02 Dec 2022 19:47:03:  7000000 
INFO  @ Fri, 02 Dec 2022 19:47:05:  8000000 
INFO  @ Fri, 02 Dec 2022 19:47:07:  9000000 
INFO  @ Fri, 02 Dec 2022 19:47:09:  10000000 
INFO  @ Fri, 02 Dec 2022 19:47:11:  11000000 
INFO  @ Fri, 02 Dec 2022 19:47:13:  12000000 
INFO  @ Fri, 02 Dec 2022 19:47:15:  13000000 
INFO  @ Fri, 02 Dec 2022 19:47:17:  14000000 
INFO  @ Fri, 02 Dec 2022 19:47:19:  15000000 
INFO  @ Fri, 02 Dec 2022 19:47:21:  16000000 
INFO  @ Fri, 02 Dec 2022 19:47:23:  17000000 
INFO  @ Fri, 02 Dec 2022 19:47:26:  18000000 
INFO  @ Fri, 02 Dec 2022 19:47:28:  19000000 
INFO  @ Fri, 02 Dec 2022 19:47:30:  20000000 
INFO  @ Fri, 02 Dec 2022 19:47:32:  21000000 
INFO  @ Fri, 02 Dec 2022 19:47:34:  22000000 
INFO  @ Fri, 02 Dec 2022 19:47:36:  23000000 
INFO  @ Fri, 02 Dec 2022 19:47:38:  24000000 
INFO  @ Fri, 02 Dec 2022 19:47:40:  25000000 
INFO  @ Fri, 02 Dec 2022 19:47:42:  26000000 
INFO  @ Fri, 02 Dec 2022 19:47:44:  27000000 
INFO  @ Fri, 02 Dec 2022 19:47:46:  28000000 
INFO  @ Fri, 02 Dec 2022 19:47:48:  29000000 
INFO  @ Fri, 02 Dec 2022 19:47:50:  30000000 
INFO  @ Fri, 02 Dec 2022 19:47:52:  31000000 
INFO  @ Fri, 02 Dec 2022 19:47:54:  32000000 
INFO  @ Fri, 02 Dec 2022 19:47:56:  33000000 
INFO  @ Fri, 02 Dec 2022 19:47:58:  34000000 
INFO  @ Fri, 02 Dec 2022 19:48:00:  35000000 
INFO  @ Fri, 02 Dec 2022 19:48:03:  36000000 
INFO  @ Fri, 02 Dec 2022 19:48:05:  37000000 
INFO  @ Fri, 02 Dec 2022 19:48:07:  38000000 
INFO  @ Fri, 02 Dec 2022 19:48:09:  39000000 
INFO  @ Fri, 02 Dec 2022 19:48:11:  40000000 
INFO  @ Fri, 02 Dec 2022 19:48:13:  41000000 
INFO  @ Fri, 02 Dec 2022 19:48:15:  42000000 
INFO  @ Fri, 02 Dec 2022 19:48:16: #1 tag size is determined as 50 bps 
INFO  @ Fri, 02 Dec 2022 19:48:16: #1 tag size = 50.0 
INFO  @ Fri, 02 Dec 2022 19:48:16: #1  total tags in treatment: 43729125 
INFO  @ Fri, 02 Dec 2022 19:48:16: #1 user defined the maximum tags... 
INFO  @ Fri, 02 Dec 2022 19:48:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1  tags after filtering in treatment: 40711860 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1  Redundant rate of treatment: 0.07 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1  total tags in control: 41679386 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1 user defined the maximum tags... 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1  tags after filtering in control: 39821414 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1  Redundant rate of control: 0.04 
INFO  @ Fri, 02 Dec 2022 19:48:17: #1 finished! 
INFO  @ Fri, 02 Dec 2022 19:48:17: #2 Build Peak Model... 
INFO  @ Fri, 02 Dec 2022 19:48:17: #2 Skipped... 
INFO  @ Fri, 02 Dec 2022 19:48:17: #2 Use 73 as fragment length 
INFO  @ Fri, 02 Dec 2022 19:48:17: #3 Call peaks... 
INFO  @ Fri, 02 Dec 2022 19:48:17: #3 Pre-compute pvalue-qvalue table... 
INFO  @ Fri, 02 Dec 2022 19:51:13: #3 Call peaks for each chromosome... 
INFO  @ Fri, 02 Dec 2022 22:36:05: #4 Write output xls file... Eya1_peaks.xls 
INFO  @ Fri, 02 Dec 2022 22:36:05: #4 Write peak in narrowPeak format file... Eya1_peaks.narrowPeak 
INFO  @ Fri, 02 Dec 2022 22:36:05: #4 Write summits bed file... Eya1_summits.bed 
INFO  @ Fri, 02 Dec 2022 22:36:05: Done! 
In [15]:
ls -lt | head -5
total 41625352
-rw-r--r-- 1 r0823712 domain users     195259 Dec  3 02:10 Eya1_summits.bed
-rw-r--r-- 1 r0823712 domain users     299027 Dec  3 02:10 Eya1_peaks.narrowPeak
-rw-r--r-- 1 r0823712 domain users     344252 Dec  3 02:10 Eya1_peaks.xls
-rw-r--r-- 1 r0823712 domain users      99105 Dec  2 23:26 Eya1_model.r
In [16]:
cat Eya1_peaks.narrowPeak | sort -k9 -g -r | head -1000
#-k9: column 9 => -log10(qvalue) => use this to rank peaks
#-g: general format
#-r: reverse / decending on column 9
chr9	21950193	21950730	Eya1_peak_3907	1617	.	50.25843	171.22057	161.78474	344
chr15	72568544	72568871	Eya1_peak_1391	1436	.	42.95110	151.40498	143.65936	191
chr13	54970758	54971192	Eya1_peak_1104	1322	.	42.12254	139.63551	132.26416	294
chr12	42972811	42973228	Eya1_peak_893	1307	.	29.34931	138.06731	130.72491	148
chr2	34090652	34090884	Eya1_peak_2140	1264	.	40.58866	133.59843	126.41547	114
chr18	25668104	25668408	Eya1_peak_1844	1257	.	42.11032	132.84566	125.70210	156
chr15	84829444	84829795	Eya1_peak_1442	1229	.	39.17722	130.03612	122.99651	167
chr15	76521887	76522503	Eya1_peak_1403	1190	.	38.11805	125.98075	119.04048	376
chr2	33018083	33018377	Eya1_peak_2136	1167	.	32.61156	123.64287	116.77760	149
chr4	140258965	140259346	Eya1_peak_2840	1166	.	30.88234	123.47452	116.61620	164
chr4	151604517	151605412	Eya1_peak_2863	1058	.	35.54206	112.49866	105.84244	593
chr12	55600100	55600522	Eya1_peak_908	1034	.	35.36379	110.07584	103.46088	272
chr15	72689744	72690132	Eya1_peak_1392	955	.	28.04696	102.09212	95.59831	234
chr19	4988970	4989348	Eya1_peak_1955	944	.	20.34944	100.88608	94.40835	199
chr11	55607773	55608073	Eya1_peak_547	930	.	30.51480	99.53233	93.06360	156
chr11	118584817	118585200	Eya1_peak_832	923	.	31.27474	98.83235	92.38107	171
chr13	54750797	54751180	Eya1_peak_1100	906	.	28.05319	97.09444	90.67398	115
chr12	24425046	24425369	Eya1_peak_879	877	.	32.04288	94.07970	87.70155	132
chr8	84947106	84947546	Eya1_peak_3780	869	.	26.03490	93.30011	86.94456	245
chr8	14072571	14072895	Eya1_peak_3696	848	.	18.98006	91.16124	84.83669	181
chr2	157913186	157913670	Eya1_peak_2349	842	.	26.66822	90.58193	84.27095	352
chr6	121473009	121473450	Eya1_peak_3358	829	.	25.43862	89.25431	82.95869	270
chr2	153032233	153032552	Eya1_peak_2311	813	.	25.11258	87.67437	81.39782	176
chr7	6410075	6410420	Eya1_peak_3401	800	.	20.79069	86.28214	80.02242	191
chr4	136924579	136924844	Eya1_peak_2826	795	.	27.26839	85.80926	79.55814	130
chr3	113090980	113091200	Eya1_peak_2548	755	.	29.41286	81.74967	75.56110	115
chr7	24359377	24359579	Eya1_peak_3427	737	.	27.76293	79.90568	73.74100	72
chr14	63681555	63681840	Eya1_peak_1297	736	.	25.53131	79.84361	73.68126	108
chr19	42255857	42256209	Eya1_peak_2033	725	.	27.06226	78.70650	72.55489	206
chr5	112718668	112718984	Eya1_peak_3032	721	.	23.15632	78.31824	72.17134	153
chr9	4138911	4139207	Eya1_peak_3890	711	.	26.23463	77.28186	71.15418	124
chr2	39806783	39807118	Eya1_peak_2156	706	.	22.83028	76.78024	70.65681	123
chr16	95093832	95094079	Eya1_peak_1608	630	.	24.18577	69.10124	63.08654	123
chr17	21801453	21801722	Eya1_peak_1644	619	.	25.67922	67.99183	61.98738	145
chr5	33438278	33438516	Eya1_peak_2924	618	.	25.60002	67.85880	61.85963	105
chr9	87021731	87021947	Eya1_peak_4038	612	.	24.69336	67.23691	61.24576	93
chr11	103920708	103921013	Eya1_peak_776	611	.	25.16314	67.12453	61.13711	140
chr7	60974266	60974421	Eya1_peak_3504	603	.	25.21251	66.30712	60.32706	85
chr4	134020693	134020964	Eya1_peak_2811	602	.	20.54798	66.19703	60.22091	142
chr1	173361728	173361968	Eya1_peak_188	586	.	24.74581	64.63068	58.68313	143
chr18	82418879	82419138	Eya1_peak_1934	579	.	23.25796	63.90534	57.96687	125
chr4	131115341	131115587	Eya1_peak_2793	574	.	14.67630	63.41300	57.48396	126
chr9	20857160	20857410	Eya1_peak_3902	573	.	19.89590	63.23513	57.30730	132
chr2	23291134	23291439	Eya1_peak_2090	548	.	22.41256	60.70183	54.81893	91
chr4	152799446	152799805	Eya1_peak_2872	542	.	22.55920	60.07499	54.20254	160
chr4	127173606	127173795	Eya1_peak_2771	532	.	21.98986	59.11264	53.25558	107
chr2	38418040	38418332	Eya1_peak_2151	513	.	15.65552	57.19809	51.37165	113
chr15	74076016	74076321	Eya1_peak_1397	509	.	22.11723	56.73942	50.91861	92
chr14	64568660	64568878	Eya1_peak_1300	495	.	20.28716	55.35202	49.54937	103
chr4	151288930	151289470	Eya1_peak_2862	477	.	20.21166	53.53451	47.75451	224
chr17	56242073	56242333	Eya1_peak_1761	462	.	14.67739	51.97838	46.21926	84
chr9	108826579	108827252	Eya1_peak_4099	456	.	10.48307	51.41437	45.66501	492
chr4	155859355	155859714	Eya1_peak_2885	449	.	14.43286	50.69167	44.94870	209
chr4	127619949	127620180	Eya1_peak_2772	440	.	19.03096	49.76420	44.03493	98
chr8	9635324	9635499	Eya1_peak_3685	431	.	16.63547	48.88451	43.16126	104
chr10	126681028	126681354	Eya1_peak_410	416	.	19.02312	47.36283	41.66317	194
chr2	172241111	172241320	Eya1_peak_2396	415	.	18.95906	47.25429	41.55551	96
chrX	73869425	73869643	Eya1_peak_4148	404	.	15.98338	46.11438	40.42768	124
chr2	136714189	136714441	Eya1_peak_2295	395	.	18.67864	45.22366	39.55022	118
chr13	100210558	100210856	Eya1_peak_1176	395	.	18.67864	45.22366	39.55022	182
chr8	112128884	112129121	Eya1_peak_3851	390	.	17.90501	44.68640	39.02437	144
chr6	113852455	113852686	Eya1_peak_3335	387	.	16.00205	44.45275	38.79247	95
chr11	115052277	115052540	Eya1_peak_811	386	.	16.80700	44.34334	38.68575	145
chr2	98330084	98330282	Eya1_peak_2236	380	.	17.34015	43.72436	38.07537	136
chr19	10403190	10403441	Eya1_peak_2000	377	.	15.00525	43.38076	37.73551	104
chr14	63713049	63713362	Eya1_peak_1298	377	.	15.00525	43.38076	37.73551	174
chr2	26208194	26208359	Eya1_peak_2102	374	.	15.64662	43.05243	37.42109	94
chr9	99218353	99218632	Eya1_peak_4055	370	.	17.18858	42.70224	37.07518	114
chr7	26489611	26489815	Eya1_peak_3440	370	.	17.60557	42.64975	37.02302	72
chr12	102555085	102555314	Eya1_peak_993	364	.	14.67921	42.02814	36.40963	165
chr7	44770095	44770391	Eya1_peak_3484	362	.	12.72113	41.90360	36.28923	127
chr5	137030208	137030384	Eya1_peak_3133	353	.	14.49327	40.94573	35.34446	89
chr5	121078610	121078834	Eya1_peak_3071	352	.	9.08574	40.83679	35.23641	124
chr4	21712175	21712488	Eya1_peak_2620	351	.	16.92642	40.75261	35.15400	187
chr4	138597875	138598053	Eya1_peak_2833	349	.	16.81469	40.56401	34.97348	114
chr8	19784691	19785123	Eya1_peak_3697	348	.	7.02673	40.44539	34.85579	121
chr7	122670868	122671111	Eya1_peak_3603	347	.	15.39721	40.36196	34.77254	74
chr2	28916126	28916366	Eya1_peak_2115	347	.	15.39721	40.36196	34.77254	105
chr14	37016042	37016212	Eya1_peak_1253	341	.	15.45479	39.72226	34.13923	63
chr15	78119783	78120090	Eya1_peak_1415	338	.	12.23207	39.46757	33.88812	105
chr9	46642808	46642992	Eya1_peak_3940	337	.	16.07206	39.30610	33.73384	90
chr4	140283501	140283714	Eya1_peak_2841	337	.	16.07206	39.30610	33.73384	109
chr9	58060892	58061158	Eya1_peak_3975	328	.	15.95129	38.36762	32.80733	180
chr11	4949326	4949562	Eya1_peak_448	324	.	13.70108	38.02962	32.47639	78
chr17	22230834	22231100	Eya1_peak_1645	320	.	16.34512	37.58119	32.03758	145
chr4	148229755	148229958	Eya1_peak_2852	316	.	10.37253	37.18806	31.64943	95
chr5	120424128	120424289	Eya1_peak_3068	315	.	15.21730	37.12100	31.58309	62
chr8	93469733	93470024	Eya1_peak_3801	311	.	13.37504	36.71734	31.18786	158
chr6	45059214	45059366	Eya1_peak_3226	305	.	15.87841	36.08903	30.57407	82
chr15	26309751	26309933	Eya1_peak_1356	305	.	15.87841	36.08903	30.57407	119
chr6	55108441	55108645	Eya1_peak_3269	303	.	11.25394	35.88099	30.36961	82
chr11	104549983	104550479	Eya1_peak_782	302	.	15.23656	35.72169	30.21530	319
chr4	68955762	68955896	Eya1_peak_2683	300	.	14.29633	35.53844	30.03566	64
chr16	10501954	10502129	Eya1_peak_1509	295	.	14.80396	34.99198	29.50060	61
chr3	87884941	87885569	Eya1_peak_2484	288	.	14.84972	34.36705	28.88548	441
chr6	58330806	58331040	Eya1_peak_3270	287	.	14.35122	34.22439	28.74503	125
chr2	125135862	125136059	Eya1_peak_2277	286	.	13.91018	34.16715	28.68899	87
chr6	30048230	30048518	Eya1_peak_3203	286	.	14.30746	34.14996	28.67266	82
chr4	136907186	136907333	Eya1_peak_2825	285	.	14.22075	34.00229	28.53130	58
chr6	72898765	72899691	Eya1_peak_3284	283	.	14.51866	33.81026	28.34087	775
chr1	25228697	25228890	Eya1_peak_17	282	.	14.89857	33.75362	28.28517	70
chr9	20813141	20813267	Eya1_peak_3901	281	.	12.83324	33.64385	28.17731	66
chr11	83421428	83421554	Eya1_peak_677	275	.	14.07054	33.05334	27.59762	55
chr19	10525247	10525736	Eya1_peak_2001	274	.	14.41325	32.94181	27.48695	268
chr7	30484368	30484466	Eya1_peak_3459	273	.	12.39691	32.84577	27.39436	51
chr17	25400556	25400717	Eya1_peak_1656	273	.	12.39691	32.84577	27.39436	94
chr6	113193842	113194095	Eya1_peak_3329	272	.	14.27376	32.70791	27.26443	70
chr6	8948576	8948727	Eya1_peak_3190	267	.	13.14519	32.15192	26.71788	64
chr18	25500579	25500731	Eya1_peak_1843	266	.	13.52773	32.13007	26.69690	48
chr1	72537068	72537240	Eya1_peak_66	262	.	14.47829	31.69182	26.26226	111
chr14	37068649	37068846	Eya1_peak_1254	262	.	14.47829	31.69182	26.26226	84
chr5	144491402	144491686	Eya1_peak_3163	261	.	12.07087	31.57795	26.15277	84
chr15	101473072	101473202	Eya1_peak_1486	261	.	12.07087	31.57795	26.15277	57
chr3	87993579	87993708	Eya1_peak_2488	261	.	13.97678	31.52990	26.10957	66
chr12	81206308	81206435	Eya1_peak_956	260	.	14.33409	31.45238	26.03709	72
chr5	135806797	135806931	Eya1_peak_3125	258	.	14.23591	31.28930	25.87558	72
chr12	88709454	88709575	Eya1_peak_978	257	.	14.13906	31.12839	25.71800	53
chr9	58841786	58841938	Eya1_peak_3977	254	.	13.99624	30.89097	25.48275	60
chr4	126655447	126655657	Eya1_peak_2766	250	.	13.71907	30.42971	25.02945	59
chr5	115731372	115731591	Eya1_peak_3049	248	.	13.62911	30.27981	24.88590	137
chr9	104569427	104569631	Eya1_peak_4070	248	.	14.01159	30.25391	24.86043	102
chr4	125300595	125300847	Eya1_peak_2758	247	.	10.03128	30.09674	24.71084	137
chr8	22859490	22859713	Eya1_peak_3705	247	.	13.12190	30.09380	24.71033	180
chr5	37243471	37243665	Eya1_peak_2940	242	.	8.80753	29.63080	24.25261	125
chr4	137676185	137676333	Eya1_peak_2828	241	.	12.80853	29.56308	24.18592	72
chr15	84965682	84965843	Eya1_peak_1445	240	.	12.73251	29.43390	24.06037	92
chr11	100758919	100759198	Eya1_peak_759	240	.	13.11315	29.41768	24.04565	109
chr11	75173488	75173618	Eya1_peak_630	240	.	13.49962	29.40532	24.03437	59
chr17	25813614	25813805	Eya1_peak_1657	237	.	12.54635	29.11680	23.74757	94
chr3	89159263	89159459	Eya1_peak_2495	237	.	11.41879	29.07822	23.70951	77
chr15	102470653	102471186	Eya1_peak_1492	237	.	11.41879	29.07822	23.70951	287
chr11	55810855	55811011	Eya1_peak_548	237	.	11.41879	29.07822	23.70951	82
chr14	79769758	79769951	Eya1_peak_1323	236	.	9.78675	28.97095	23.60823	104
chr1	63113477	63114377	Eya1_peak_59	234	.	13.54488	28.83068	23.47242	375
chr10	115184917	115185071	Eya1_peak_387	234	.	13.54488	28.83068	23.47242	84
chr7	28263918	28264083	Eya1_peak_3446	234	.	13.14667	28.81904	23.46490	93
chr2	129715789	129715958	Eya1_peak_2288	234	.	12.75112	28.80957	23.45582	92
chr5	134638803	134639293	Eya1_peak_3119	233	.	12.71212	28.74388	23.39314	424
chr2	79454293	79454427	Eya1_peak_2207	233	.	12.71212	28.74388	23.39314	67
chr9	64666646	64666840	Eya1_peak_4001	233	.	13.06130	28.67699	23.32736	123
chr10	60445228	60445536	Eya1_peak_279	230	.	10.39995	28.40549	23.05923	166
chr10	127256182	127256343	Eya1_peak_417	229	.	12.85264	28.32931	22.98425	87
chr8	20296773	20297361	Eya1_peak_3701	227	.	7.43917	28.14086	22.79840	290
chr18	42396150	42396368	Eya1_peak_1883	227	.	12.69046	28.05851	22.71919	122
chr2	25318878	25319146	Eya1_peak_2095	226	.	12.65055	27.99180	22.65529	141
chr2	180104445	180104659	Eya1_peak_2413	225	.	11.09274	27.84700	22.51441	136
chr15	80277767	80277892	Eya1_peak_1428	223	.	12.83461	27.65584	22.33058	70
chr17	72603209	72603409	Eya1_peak_1785	223	.	11.69167	27.64426	22.31924	95
chr5	36836090	36836213	Eya1_peak_2935	221	.	11.97941	27.50118	22.17908	66
chr1	38939741	38939850	Eya1_peak_30	221	.	12.70877	27.44721	22.12621	49
chr19	35833124	35833289	Eya1_peak_2021	221	.	13.07818	27.42266	22.10222	69
chr1	70725721	70725836	Eya1_peak_65	221	.	13.07818	27.42266	22.10222	58
chr16	17201070	17201443	Eya1_peak_1523	221	.	13.07818	27.42266	22.10222	160
chr12	112141406	112141544	Eya1_peak_1014	221	.	13.07818	27.42266	22.10222	82
chr2	178277338	178277447	Eya1_peak_2404	220	.	12.66737	27.37853	22.06355	54
chr13	25269142	25269418	Eya1_peak_1064	220	.	12.66737	27.37853	22.06355	100
chr17	87798525	87798678	Eya1_peak_1811	214	.	11.93728	26.79274	21.48707	61
chr5	27737222	27737424	Eya1_peak_2905	214	.	9.29768	26.75250	21.44795	114
chr7	121596533	121596651	Eya1_peak_3600	214	.	12.26775	26.71403	21.41153	64
chr2	70559664	70559781	Eya1_peak_2186	214	.	12.26775	26.71403	21.41153	41
chr8	124793291	124793482	Eya1_peak_3879	213	.	12.60031	26.63480	21.33681	130
chr9	56738429	56738534	Eya1_peak_3961	213	.	10.76670	26.62870	21.33154	38
chr2	29573696	29573853	Eya1_peak_2117	213	.	10.76670	26.62870	21.33154	85
chr7	25146039	25146178	Eya1_peak_3432	211	.	12.11488	26.45898	21.16973	65
chr6	113881919	113882081	Eya1_peak_3336	210	.	11.32656	26.37718	21.08873	127
chr4	125590607	125590770	Eya1_peak_2761	210	.	12.39238	26.29144	21.00438	63
chr11	35798959	35799121	Eya1_peak_502	210	.	12.39238	26.29144	21.00438	110
chr4	155397640	155397757	Eya1_peak_2881	208	.	11.89258	26.08712	20.80503	54
chr3	91213400	91213576	Eya1_peak_2505	207	.	12.61147	26.03038	20.74978	55
chr1	8123236	8123343	Eya1_peak_5	207	.	12.61147	26.03038	20.74978	55
chr16	7740516	7740654	Eya1_peak_1502	207	.	12.61147	26.03038	20.74978	70
chr1	75263096	75263292	Eya1_peak_74	204	.	12.07359	25.76395	20.49252	48
chr1	127496887	127497019	Eya1_peak_116	204	.	11.67829	25.72738	20.45681	69
chr8	20424068	20424639	Eya1_peak_3702	203	.	5.21851	25.62575	20.35870	379
chr2	179193798	179193992	Eya1_peak_2408	202	.	8.02502	25.52196	20.25605	106
chr9	108190094	108190226	Eya1_peak_4087	202	.	11.53967	25.49394	20.22894	64
chr14	32597330	32597466	Eya1_peak_1243	202	.	11.53967	25.49394	20.22894	69
chr2	77945609	77946094	Eya1_peak_2205	201	.	8.00102	25.46328	20.19978	414
chr7	79499292	79499495	Eya1_peak_3520	201	.	10.44066	25.42371	20.16041	140
chr15	84086472	84086599	Eya1_peak_1440	201	.	10.44066	25.42371	20.16041	58
chr9	57606124	57606281	Eya1_peak_3969	199	.	12.11002	25.20601	19.95392	96
chr17	27466780	27466908	Eya1_peak_1664	198	.	11.69745	25.13922	19.88793	64
chr19	53390108	53390437	Eya1_peak_2055	198	.	10.96145	25.12429	19.87337	258
chr4	125835363	125835501	Eya1_peak_2762	196	.	11.95014	24.94278	19.69465	66
chr1	39900911	39901328	Eya1_peak_35	196	.	11.95014	24.94278	19.69465	356
chr14	80215912	80216097	Eya1_peak_1326	195	.	11.48281	24.78126	19.53751	123
chr12	51829066	51829562	Eya1_peak_898	195	.	11.48281	24.78126	19.53751	443
chr7	110701763	110701977	Eya1_peak_3573	194	.	11.79444	24.68611	19.44514	150
chr8	84454688	84454862	Eya1_peak_3773	194	.	12.14477	24.65444	19.41604	55
chrX	15963125	15963239	Eya1_peak_4147	193	.	8.80862	24.58018	19.34808	69
chr2	156652957	156653099	Eya1_peak_2337	193	.	8.80862	24.58018	19.34808	69
chr7	18951534	18951660	Eya1_peak_3420	192	.	11.64273	24.43570	19.20666	54
chr15	79791635	79791834	Eya1_peak_1422	192	.	11.27590	24.43500	19.20636	85
chr5	137031177	137031280	Eya1_peak_3135	191	.	10.89316	24.39605	19.16798	49
chr3	114904085	114904296	Eya1_peak_2550	190	.	10.11461	24.23245	19.00677	139
chr1	146106902	146107194	Eya1_peak_149	190	.	10.11461	24.23245	19.00677	151
chr11	33680216	33680365	Eya1_peak_498	190	.	10.11461	24.23245	19.00677	65
chr10	81037459	81037598	Eya1_peak_339	190	.	10.11461	24.23245	19.00677	70
chr6	86525398	86526161	Eya1_peak_3305	189	.	11.49488	24.19125	18.97339	559
chr11	101602624	101602774	Eya1_peak_761	189	.	11.49488	24.19125	18.97339	61
chr4	103572053	103572216	Eya1_peak_2714	188	.	11.42235	24.07118	18.85390	101
chr8	20550250	20550675	Eya1_peak_3703	186	.	7.00446	23.88376	18.67354	235
chr8	84687230	84687871	Eya1_peak_3776	185	.	11.58438	23.73598	18.52746	380
chr6	95223626	95223782	Eya1_peak_3322	185	.	11.58438	23.73598	18.52746	51
chr5	52189936	52190422	Eya1_peak_2949	185	.	11.58438	23.73598	18.52746	282
chr3	89764407	89764587	Eya1_peak_2498	184	.	10.82095	23.66871	18.46150	60
chr2	155775683	155775849	Eya1_peak_2331	184	.	11.17557	23.66171	18.45594	107
chr1	74891632	74891795	Eya1_peak_72	184	.	11.50791	23.61046	18.40484	91
chr7	138084022	138084287	Eya1_peak_3664	183	.	8.56409	23.51211	18.30942	143
chr11	51606042	51606778	Eya1_peak_526	182	.	11.07303	23.49114	18.29048	346
chr19	47006443	47006633	Eya1_peak_2049	182	.	11.43245	23.48652	18.28747	83
chr13	9763667	9764552	Eya1_peak_1030	182	.	11.39508	23.42512	18.22775	568
chr7	122969970	122970710	Eya1_peak_3604	181	.	11.35797	23.36411	18.16800	183
chr3	19694584	19694718	Eya1_peak_2438	181	.	11.35797	23.36411	18.16800	60
chrX	147639717	147639944	Eya1_peak_4157	181	.	11.67806	23.29548	18.10246	77
chr5	116914996	116915148	Eya1_peak_3059	181	.	11.67806	23.29548	18.10246	79
chr4	12171396	12171804	Eya1_peak_2614	181	.	11.67806	23.29548	18.10246	135
chr18	76847502	76847618	Eya1_peak_1924	181	.	11.67806	23.29548	18.10246	51
chr10	41071875	41071989	Eya1_peak_259	181	.	11.67806	23.29548	18.10246	50
chr2	143546889	143547023	Eya1_peak_2298	179	.	11.24805	23.18331	17.99706	70
chr11	74619244	74619433	Eya1_peak_619	179	.	11.60176	23.17092	17.98487	107
chr15	78066632	78066758	Eya1_peak_1414	179	.	11.21188	23.12377	17.93847	77
chr9	43959624	43959808	Eya1_peak_3926	178	.	9.78857	23.05537	17.87166	93
chr8	84471316	84471557	Eya1_peak_3774	178	.	9.78857	23.05537	17.87166	160
chr8	123041391	123042236	Eya1_peak_3872	178	.	10.80859	23.04981	17.87166	435
chr5	141985168	141985312	Eya1_peak_3152	178	.	9.78857	23.05537	17.87166	70
chr4	140439952	140440172	Eya1_peak_2843	178	.	9.78857	23.05537	17.87166	138
chr2	21367380	21367566	Eya1_peak_2087	178	.	9.78857	23.05537	17.87166	81
chr2	180756015	180756195	Eya1_peak_2419	178	.	9.78857	23.05537	17.87166	88
chr17	73488011	73488159	Eya1_peak_1788	178	.	9.78857	23.05537	17.87166	82
chr15	89453390	89453557	Eya1_peak_1457	178	.	6.85054	22.98327	17.80807	118
chr12	105322217	105322521	Eya1_peak_998	177	.	11.10475	22.94730	17.77261	233
chr14	27596431	27596562	Eya1_peak_1227	177	.	10.74444	22.94242	17.76820	47
chr11	99229979	99230488	Eya1_peak_753	177	.	10.74444	22.94242	17.76820	310
chr4	44511811	44511959	Eya1_peak_2651	177	.	11.44337	22.91233	17.73956	76
chr1	37218519	37218691	Eya1_peak_26	177	.	11.44337	22.91233	17.73956	62
chr18	7869685	7870098	Eya1_peak_1826	176	.	11.40444	22.84877	17.67680	345
chr9	106656272	106656432	Eya1_peak_4077	176	.	10.99965	22.77395	17.60241	49
chr6	87850370	87850956	Eya1_peak_3308	176	.	10.99965	22.77395	17.60241	119
chr2	156179609	156180148	Eya1_peak_2334	176	.	10.99965	22.77395	17.60241	371
chr4	136601978	136602323	Eya1_peak_2823	174	.	11.28924	22.66059	17.49288	249
chr4	129120917	129121245	Eya1_peak_2779	174	.	11.28924	22.66059	17.49288	148
chr14	49172427	49172680	Eya1_peak_1265	174	.	11.28924	22.66059	17.49288	183
chr1	134664961	134665103	Eya1_peak_136	174	.	11.28924	22.66059	17.49288	46
chr18	38075457	38075672	Eya1_peak_1875	173	.	11.21372	22.53719	17.37366	69
chr7	4178527	4178727	Eya1_peak_3395	172	.	8.31956	22.45657	17.29459	85
chr4	9269493	9269622	Eya1_peak_2608	172	.	8.31956	22.45657	17.29459	64
chr8	74993632	74994201	Eya1_peak_3758	172	.	10.79532	22.43619	17.27610	287
chr11	102393330	102393560	Eya1_peak_768	171	.	10.72888	22.32615	17.16902	157
chr4	132211312	132212032	Eya1_peak_2797	171	.	10.69597	22.27159	17.11521	567
chr9	97110678	97111065	Eya1_peak_4052	170	.	10.66326	22.21734	17.06153	153
chr8	110196824	110196940	Eya1_peak_3844	170	.	10.66326	22.21734	17.06153	64
chr11	6016490	6016608	Eya1_peak_456	170	.	10.66326	22.21734	17.06153	49
chr9	59578343	59578528	Eya1_peak_3984	169	.	10.92150	22.05908	16.90788	94
chr5	111901765	111901956	Eya1_peak_3027	169	.	10.92150	22.05908	16.90788	132
chr3	82412562	82412651	Eya1_peak_2482	169	.	10.92150	22.05908	16.90788	45
chr9	27308178	27308324	Eya1_peak_3913	168	.	11.21136	21.95418	16.80686	65
chr8	111941263	111941458	Eya1_peak_3850	168	.	10.50266	21.95053	16.80686	124
chr18	66561051	66561213	Eya1_peak_1911	168	.	11.21136	21.95418	16.80686	113
chr11	56812248	56812393	Eya1_peak_550	168	.	11.21136	21.95418	16.80686	97
chr8	121736355	121736468	Eya1_peak_3866	167	.	10.14249	21.92714	16.78704	50
chr5	146644638	146644821	Eya1_peak_3169	167	.	11.17678	21.89794	16.75844	111
chr7	16147765	16147930	Eya1_peak_3410	167	.	9.46253	21.89293	16.75402	76
chr7	131960671	131960827	Eya1_peak_3652	167	.	9.46253	21.89293	16.75402	70
chr4	124317179	124317369	Eya1_peak_2754	167	.	9.46253	21.89293	16.75402	95
chr17	27228668	27228818	Eya1_peak_1663	167	.	9.46253	21.89293	16.75402	72
chr16	35302506	35303112	Eya1_peak_1564	167	.	9.46253	21.89293	16.75402	40
chr11	98314191	98314325	Eya1_peak_744	167	.	9.46253	21.89293	16.75402	69
chr10	79718075	79718250	Eya1_peak_315	167	.	9.46253	21.89293	16.75402	63
chr10	29146977	29147095	Eya1_peak_243	167	.	9.46253	21.89293	16.75402	56
chr11	82514890	82515002	Eya1_peak_675	165	.	10.34683	21.69085	16.56532	51
chr8	71483976	71484105	Eya1_peak_3751	163	.	10.57695	21.49368	16.37304	47
chr14	121378690	121379149	Eya1_peak_1343	163	.	10.57695	21.49368	16.37304	281
chr4	152287046	152287180	Eya1_peak_2869	163	.	10.22545	21.48801	16.36997	67
chr9	66307432	66307657	Eya1_peak_4009	162	.	8.07502	21.41391	16.29678	96
chr10	112928514	112928962	Eya1_peak_386	162	.	8.07502	21.41391	16.29678	242
chr4	81442452	81442762	Eya1_peak_2688	162	.	10.83807	21.34694	16.23245	270
chr18	77417640	77417764	Eya1_peak_1928	162	.	10.83807	21.34694	16.23245	53
chr1	192472442	192472628	Eya1_peak_215	162	.	10.83807	21.34694	16.23245	133
chr11	59584686	59584797	Eya1_peak_561	162	.	10.83807	21.34694	16.23245	47
chr2	180417826	180417975	Eya1_peak_2415	161	.	10.10689	21.28935	16.17681	97
chr13	99900547	99900724	Eya1_peak_1175	161	.	10.80170	21.28774	16.17522	78
chr7	90442829	90443670	Eya1_peak_3542	161	.	10.76558	21.22892	16.11720	179
chr4	131658046	131658174	Eya1_peak_2794	160	.	10.72969	21.17048	16.06041	57
chr18	63977172	63977328	Eya1_peak_1906	160	.	10.72969	21.17048	16.06041	67
chr17	74528981	74529113	Eya1_peak_1793	160	.	10.72969	21.17048	16.06041	62
chr9	110532687	110533379	Eya1_peak_4104	160	.	10.34843	21.11728	16.00886	251
chr12	86213191	86213346	Eya1_peak_970	160	.	10.69404	21.11242	16.00449	67
chr7	129469619	129469785	Eya1_peak_3646	158	.	10.62345	20.99741	15.89252	66
chr8	9769203	9769332	Eya1_peak_3686	158	.	10.25349	20.96051	15.85626	31
chr8	95331431	95331779	Eya1_peak_3812	158	.	10.25349	20.96051	15.85626	278
chr5	116714391	116714511	Eya1_peak_3057	158	.	10.25349	20.96051	15.85626	70
chr4	136311048	136311558	Eya1_peak_2821	158	.	10.25349	20.96051	15.85626	84
chr19	41661111	41661246	Eya1_peak_2030	156	.	10.12957	20.75550	15.65942	63
chr11	60105176	60106260	Eya1_peak_563	156	.	10.12957	20.75550	15.65942	191
chr4	153679297	153679421	Eya1_peak_2875	156	.	9.13649	20.74566	15.64987	60
chr4	127021372	127022284	Eya1_peak_2770	156	.	9.13649	20.74566	15.64987	368
chr2	167188823	167189204	Eya1_peak_2386	156	.	9.13649	20.74566	15.64987	260
chr19	6502708	6502895	Eya1_peak_1977	156	.	9.13649	20.74566	15.64987	67
chr19	47016608	47016760	Eya1_peak_2050	156	.	9.13649	20.74566	15.64987	51
chr17	91092801	91092976	Eya1_peak_1816	156	.	9.13649	20.74566	15.64987	105
chr12	108994780	108994927	Eya1_peak_1006	156	.	9.13649	20.74566	15.64987	75
chr12	106115158	106115318	Eya1_peak_1000	156	.	9.13649	20.74566	15.64987	70
chr12	102550607	102550779	Eya1_peak_992	156	.	9.13649	20.74566	15.64987	94
chr11	83417206	83417312	Eya1_peak_676	156	.	9.13649	20.74566	15.64987	55
chr1	152956322	152956491	Eya1_peak_155	156	.	9.13649	20.74566	15.64987	89
chr5	135843519	135843678	Eya1_peak_3126	156	.	10.45098	20.71614	15.63094	90
chr5	113407464	113407592	Eya1_peak_3035	156	.	10.45098	20.71614	15.63094	70
chr4	153357659	153357770	Eya1_peak_2874	156	.	9.76715	20.71686	15.63094	52
chr9	54271039	54271153	Eya1_peak_3955	155	.	10.74465	20.63129	15.54729	29
chr7	59228997	59229530	Eya1_peak_3503	155	.	10.74465	20.63129	15.54729	201
chr5	63689227	63689318	Eya1_peak_2955	155	.	10.74465	20.63129	15.54729	54
chr2	154076391	154076499	Eya1_peak_2317	155	.	10.74465	20.63129	15.54729	51
chr16	33251451	33251775	Eya1_peak_1560	154	.	9.35622	20.57506	15.49982	72
chr2	80580522	80581095	Eya1_peak_2209	154	.	10.35017	20.55151	15.47678	387
chr7	123235571	123235699	Eya1_peak_3607	154	.	10.67445	20.51757	15.44345	70
chr11	105182016	105182537	Eya1_peak_784	154	.	9.00442	20.50887	15.43542	292
chr6	92091693	92092047	Eya1_peak_3319	154	.	10.31699	20.49730	15.42400	75
chr12	3806298	3806724	Eya1_peak_856	154	.	10.31699	20.49730	15.42400	295
chr2	26205178	26205345	Eya1_peak_2101	153	.	9.94922	20.45624	15.38370	131
chr2	119477302	119477631	Eya1_peak_2266	153	.	9.94922	20.45624	15.38370	48
chr12	3955550	3955646	Eya1_peak_861	153	.	9.94922	20.45624	15.38370	61
chr7	24727773	24727900	Eya1_peak_3428	153	.	10.28403	20.44342	15.37248	62
chr2	172320988	172321167	Eya1_peak_2397	153	.	10.25128	20.38986	15.31972	112
chr4	141139345	141139666	Eya1_peak_2846	152	.	10.21873	20.33661	15.26927	242
chr2	163889528	163889648	Eya1_peak_2368	151	.	10.15425	20.23107	15.16580	62
chr12	80435129	80435444	Eya1_peak_948	151	.	10.15425	20.23107	15.16580	168
chr2	157663726	157663873	Eya1_peak_2348	149	.	10.38691	20.05170	14.99107	82
chr15	8443802	8444267	Eya1_peak_1346	149	.	10.38691	20.05170	14.99107	233
chr2	91921278	91921406	Eya1_peak_2222	149	.	9.69041	20.02477	14.96701	67
chr2	154436633	154436974	Eya1_peak_2318	149	.	10.02772	20.02365	14.96592	59
chr7	44335740	44335866	Eya1_peak_3482	149	.	10.35205	19.99519	14.93797	61
chr15	73026826	73027022	Eya1_peak_1393	149	.	10.35205	19.99519	14.93797	107
chr1	167079655	167079740	Eya1_peak_181	148	.	9.96562	19.92173	14.86680	35
chr11	118685587	118685695	Eya1_peak_835	148	.	10.28304	19.88329	14.82890	55
chr9	63151246	63151354	Eya1_peak_3993	147	.	9.24898	19.83296	14.78078	52
chr4	151186524	151186729	Eya1_peak_2861	147	.	9.24898	19.83296	14.78078	97
chr8	126404662	126404774	Eya1_peak_3882	147	.	10.24887	19.82787	14.77639	56
chr3	90508983	90509410	Eya1_peak_2504	147	.	10.21493	19.77282	14.72249	221
chr10	80399072	80399394	Eya1_peak_330	147	.	10.21493	19.77282	14.72249	104
chr5	143527509	143527983	Eya1_peak_3161	146	.	9.84371	19.72131	14.67198	301
chr4	58911660	58911939	Eya1_peak_2671	146	.	10.18122	19.71811	14.67198	154
chr11	81005975	81006074	Eya1_peak_669	146	.	9.84371	19.72131	14.67198	64
chr18	36004725	36004901	Eya1_peak_1872	146	.	10.14773	19.66375	14.61959	91
chr8	4324606	4325023	Eya1_peak_3681	145	.	8.81044	19.61410	14.57058	246
chr5	148071930	148072110	Eya1_peak_3176	145	.	8.81044	19.61410	14.57058	74
chr4	140358224	140358382	Eya1_peak_2842	145	.	8.81044	19.61410	14.57058	57
chr3	31309004	31309146	Eya1_peak_2445	145	.	8.81044	19.61410	14.57058	72
chr3	118431459	118431649	Eya1_peak_2554	145	.	8.81044	19.61410	14.57058	128
chr2	94245478	94245636	Eya1_peak_2233	145	.	10.11445	19.60974	14.57058	86
chr2	158584723	158584892	Eya1_peak_2354	145	.	8.81044	19.61410	14.57058	68
chr17	83010982	83011137	Eya1_peak_1801	145	.	8.81044	19.61410	14.57058	80
chr17	39107409	39107510	Eya1_peak_1720	145	.	8.81044	19.61410	14.57058	40
chr12	86983589	86983730	Eya1_peak_973	145	.	8.81044	19.61410	14.57058	45
chr10	89224654	89224792	Eya1_peak_361	145	.	8.81044	19.61410	14.57058	67
chr4	128042767	128042895	Eya1_peak_2774	144	.	9.39182	19.52353	14.49168	58
chr4	126202274	126202650	Eya1_peak_2763	144	.	9.39182	19.52353	14.49168	303
chr10	60914531	60914664	Eya1_peak_280	144	.	9.39182	19.52353	14.49168	56
chr15	27655140	27655234	Eya1_peak_1357	144	.	10.04856	19.50272	14.47203	55
chr12	83632295	83632904	Eya1_peak_961	144	.	10.04856	19.50272	14.47203	142
chr1	86527785	86528001	Eya1_peak_93	144	.	9.69546	19.47700	14.44978	146
chr1	74391728	74391961	Eya1_peak_68	144	.	9.69546	19.47700	14.44978	188
chr3	105275375	105275513	Eya1_peak_2540	144	.	10.01593	19.44970	14.42279	65
chr2	164968564	164968847	Eya1_peak_2375	143	.	7.58596	19.36886	14.34354	100
chr17	6321824	6322006	Eya1_peak_1629	143	.	7.58596	19.36886	14.34354	106
chr11	105181635	105181943	Eya1_peak_783	143	.	7.58596	19.36886	14.34354	206
chr6	35539670	35539817	Eya1_peak_3216	143	.	10.27795	19.32762	14.30448	61
chr12	18467145	18467323	Eya1_peak_875	143	.	10.27795	19.32762	14.30448	48
chr10	7589682	7589929	Eya1_peak_224	143	.	10.27795	19.32762	14.30448	122
chr2	179200643	179200756	Eya1_peak_2409	142	.	9.91931	19.29261	14.27566	41
chr12	112673599	112673946	Eya1_peak_1016	142	.	9.91931	19.29261	14.27566	260
chr17	80061466	80062025	Eya1_peak_1796	142	.	9.88752	19.24088	14.22487	147
chr13	99564493	99564605	Eya1_peak_1174	142	.	9.88752	19.24088	14.22487	39
chr7	123123957	123124161	Eya1_peak_3605	142	.	9.55160	19.23926	14.22408	155
chr18	25752876	25753035	Eya1_peak_1846	142	.	9.55160	19.23926	14.22408	59
chr2	157970788	157970940	Eya1_peak_2350	141	.	9.49525	19.14593	14.13433	62
chr9	64624676	64624805	Eya1_peak_4000	141	.	9.82454	19.13836	14.12684	60
chr4	129514113	129514463	Eya1_peak_2783	141	.	9.82454	19.13836	14.12684	95
chr8	86425516	86425640	Eya1_peak_3788	139	.	9.73155	18.98685	13.97791	83
chr18	77274357	77274452	Eya1_peak_1927	139	.	9.73155	18.98685	13.97791	49
chr15	86932807	86932930	Eya1_peak_1449	139	.	9.73155	18.98685	13.97791	51
chr8	123414387	123414507	Eya1_peak_3874	137	.	9.61028	18.78895	13.78484	71
chr9	57764834	57765104	Eya1_peak_3973	137	.	9.27633	18.78221	13.77869	114
chr4	32601239	32601381	Eya1_peak_2624	137	.	9.27633	18.78221	13.77869	90
chr4	148293339	148293553	Eya1_peak_2854	137	.	9.27633	18.78221	13.77869	132
chr2	174330206	174330835	Eya1_peak_2402	137	.	9.27633	18.78221	13.77869	573
chr14	46788088	46788265	Eya1_peak_1260	137	.	9.27633	18.78221	13.77869	98
chr7	124199057	124199195	Eya1_peak_3609	137	.	9.93574	18.77567	13.77311	72
chr4	136144090	136144289	Eya1_peak_2819	137	.	9.24967	18.73779	13.73852	39
chr8	119258689	119258895	Eya1_peak_3859	136	.	9.83638	18.61530	13.61923	93
chr16	91647901	91648371	Eya1_peak_1601	136	.	9.83638	18.61530	13.61923	175
chr2	92401271	92401451	Eya1_peak_2226	135	.	9.80370	18.56254	13.56738	118
chr11	72607632	72607775	Eya1_peak_615	135	.	9.80370	18.56254	13.56738	95
chr5	121712411	121712827	Eya1_peak_3075	135	.	9.77123	18.51012	13.51636	357
chr7	7080954	7081184	Eya1_peak_3402	135	.	8.48440	18.49883	13.50733	54
chr7	33836732	33836956	Eya1_peak_3467	135	.	8.48440	18.49883	13.50733	107
chr7	144294418	144294512	Eya1_peak_3675	135	.	8.48440	18.49883	13.50733	46
chr7	118001237	118001389	Eya1_peak_3588	135	.	8.48440	18.49883	13.50733	65
chr6	89242479	89242586	Eya1_peak_3315	135	.	8.48440	18.49883	13.50733	64
chr4	153189629	153189775	Eya1_peak_2873	135	.	8.48440	18.49883	13.50733	95
chr4	139059694	139059859	Eya1_peak_2834	135	.	8.48440	18.49883	13.50733	100
chr2	25608099	25608412	Eya1_peak_2099	135	.	9.43394	18.50051	13.50733	123
chr18	64042669	64042829	Eya1_peak_1907	135	.	8.48440	18.49883	13.50733	67
chr17	46856876	46857518	Eya1_peak_1749	135	.	8.48440	18.49883	13.50733	226
chr1	178336968	178337653	Eya1_peak_197	135	.	9.43394	18.50051	13.50733	344
chr11	52099015	52099210	Eya1_peak_530	135	.	9.43394	18.50051	13.50733	58
chr9	113707834	113708186	Eya1_peak_4110	134	.	9.73899	18.45803	13.47895	210
chr7	81493354	81493552	Eya1_peak_3534	134	.	9.73899	18.45803	13.47895	137
chr18	77774149	77774437	Eya1_peak_1929	134	.	9.40518	18.45338	13.47508	88
chr8	10255830	10256031	Eya1_peak_3687	133	.	7.34143	18.36732	13.39028	87
chr6	127767904	127768115	Eya1_peak_3373	133	.	7.34143	18.36732	13.39028	54
chr2	93071776	93071900	Eya1_peak_2230	133	.	7.34143	18.36732	13.39028	72
chr2	31346212	31346375	Eya1_peak_2126	133	.	7.34143	18.36732	13.39028	62
chr8	13106013	13106320	Eya1_peak_3694	133	.	9.67512	18.35484	13.38054	145
chr9	45984334	45984800	Eya1_peak_3938	133	.	9.01648	18.34783	13.37449	112
chr9	105693984	105694064	Eya1_peak_4073	133	.	9.01648	18.34783	13.37449	41
chr5	137553469	137553764	Eya1_peak_3141	133	.	9.01648	18.34783	13.37449	97
chr16	33380972	33381467	Eya1_peak_1561	133	.	9.64350	18.30373	13.33243	194
chr1	133025109	133025353	Eya1_peak_126	133	.	8.66374	18.28217	13.31144	66
chr9	100023787	100023888	Eya1_peak_4057	132	.	9.61209	18.25295	13.28294	40
chr6	89070121	89070258	Eya1_peak_3314	132	.	9.61209	18.25295	13.28294	46
chr16	34400465	34400607	Eya1_peak_1563	131	.	9.51906	18.10246	13.13620	48
chr4	124882440	124882530	Eya1_peak_2757	130	.	9.48845	18.05291	13.08723	43
chr7	57592312	57592438	Eya1_peak_3502	130	.	9.15399	18.04067	13.07905	61
chr6	35539348	35539619	Eya1_peak_3215	130	.	9.81124	18.04406	13.07905	199
chr4	89313629	89313752	Eya1_peak_2695	130	.	9.81124	18.04406	13.07905	66
chr4	8536050	8536394	Eya1_peak_2607	130	.	9.15399	18.04067	13.07905	127
chr3	152821318	152821453	Eya1_peak_2593	130	.	9.15399	18.04067	13.07905	70
chr2	146226685	146226805	Eya1_peak_2301	130	.	9.81124	18.04406	13.07905	71
chr18	88893584	88894071	Eya1_peak_1944	130	.	9.81124	18.04406	13.07905	408
chr17	28575544	28575734	Eya1_peak_1670	130	.	9.15399	18.04067	13.07905	123
chr15	72201011	72201104	Eya1_peak_1390	130	.	9.81124	18.04406	13.07905	48
chr10	128377139	128377627	Eya1_peak_423	130	.	9.15399	18.04067	13.07905	72
chr4	42999728	43000327	Eya1_peak_2644	130	.	9.45804	18.00367	13.04851	361
chr4	148286816	148286918	Eya1_peak_2853	130	.	7.92306	18.00067	13.04664	69
chr3	145118654	145118769	Eya1_peak_2583	130	.	9.78098	17.99549	13.04153	63
chr1	131097106	131097475	Eya1_peak_119	130	.	9.78098	17.99549	13.04153	327
chr11	71937240	71937369	Eya1_peak_608	129	.	9.71352	17.88723	12.93657	62
chr11	49203617	49203769	Eya1_peak_515	129	.	9.71352	17.88723	12.93657	65
chr7	131917500	131917602	Eya1_peak_3651	128	.	9.68014	17.83365	12.88478	60
chr14	16365376	16365978	Eya1_peak_1207	128	.	9.68014	17.83365	12.88478	293
chr8	126592834	126593367	Eya1_peak_3885	128	.	9.02015	17.81987	12.87121	127
chr5	37009889	37010211	Eya1_peak_2937	128	.	9.33831	17.80962	12.86110	250
chr9	75683880	75684027	Eya1_peak_4029	128	.	9.30885	17.76183	12.81403	66
chr9	109875974	109876392	Eya1_peak_4101	128	.	9.30885	17.76183	12.81403	115
chr16	94570578	94570722	Eya1_peak_1605	128	.	9.30885	17.76183	12.81403	54
chr12	69892697	69892904	Eya1_peak_927	128	.	9.30885	17.76183	12.81403	129
chr2	4881788	4882270	Eya1_peak_2074	127	.	9.61406	17.72760	12.78270	228
chr4	124633416	124633556	Eya1_peak_2755	127	.	9.27958	17.71432	12.76956	65
chr2	172042193	172042371	Eya1_peak_2394	127	.	9.27958	17.71432	12.76956	82
chr12	31949827	31949943	Eya1_peak_889	127	.	9.58136	17.67511	12.73094	50
chr1	160906443	160907077	Eya1_peak_170	127	.	9.58136	17.67511	12.73094	207
chr6	117906848	117907607	Eya1_peak_3349	126	.	9.54888	17.62297	12.67982	248
chr12	113188123	113188230	Eya1_peak_1022	126	.	9.54888	17.62297	12.67982	57
chr8	119164207	119164292	Eya1_peak_3858	126	.	8.89018	17.60475	12.66231	45
chr7	45873277	45873604	Eya1_peak_3494	126	.	8.89018	17.60475	12.66231	262
chr6	47767735	47767890	Eya1_peak_3242	126	.	5.18064	17.60359	12.66231	96
chr5	121068818	121068935	Eya1_peak_3070	126	.	8.89018	17.60475	12.66231	77
chr11	104198019	104198141	Eya1_peak_779	126	.	8.89018	17.60475	12.66231	50
chr4	148626368	148626726	Eya1_peak_2857	126	.	7.97906	17.59257	12.65156	216
chr16	97851265	97851506	Eya1_peak_1615	126	.	9.19285	17.57345	12.63265	82
chr8	20122285	20123015	Eya1_peak_3700	126	.	3.50182	17.57015	12.63046	460
chr8	40511786	40512130	Eya1_peak_3722	125	.	9.48458	17.51974	12.58116	179
chr5	99707418	99707500	Eya1_peak_3000	125	.	9.48458	17.51974	12.58116	55
chr17	69439314	69439460	Eya1_peak_1781	125	.	9.48458	17.51974	12.58116	95
chr4	120866402	120866559	Eya1_peak_2745	125	.	9.13593	17.48089	12.54435	98
chr4	121214830	121215002	Eya1_peak_2747	124	.	9.42113	17.41786	12.48246	63
chr18	38217110	38217214	Eya1_peak_1876	124	.	9.42113	17.41786	12.48246	61
chr9	78481046	78481605	Eya1_peak_4030	124	.	8.15836	17.40049	12.46604	253
chr9	49341152	49341294	Eya1_peak_3947	124	.	8.15836	17.40049	12.46604	66
chr7	84085100	84085250	Eya1_peak_3537	124	.	8.15836	17.40049	12.46604	85
chr6	113077450	113078166	Eya1_peak_3328	124	.	8.15836	17.40049	12.46604	243
chr4	155491449	155492265	Eya1_peak_2882	124	.	8.15836	17.40049	12.46604	418
chr3	88220950	88221124	Eya1_peak_2489	124	.	8.15836	17.40049	12.46604	99
chr2	25500896	25501251	Eya1_peak_2097	124	.	8.15836	17.40049	12.46604	133
chr2	152081901	152082036	Eya1_peak_2303	124	.	8.15836	17.40049	12.46604	71
chr2	132781744	132781971	Eya1_peak_2294	124	.	8.15836	17.40049	12.46604	54
chr2	104816345	104816786	Eya1_peak_2247	124	.	8.15836	17.40049	12.46604	241
chr18	70411115	70411244	Eya1_peak_1912	124	.	8.15836	17.40049	12.46604	61
chr17	84820739	84820865	Eya1_peak_1807	124	.	8.15836	17.40049	12.46604	66
chr15	88733720	88733929	Eya1_peak_1454	124	.	8.15836	17.40049	12.46604	59
chr14	29657148	29657299	Eya1_peak_1228	124	.	8.15836	17.40049	12.46604	70
chr10	71403717	71403833	Eya1_peak_300	124	.	8.15836	17.40049	12.46604	60
chr10	4387214	4387543	Eya1_peak_219	124	.	8.15836	17.40049	12.46604	102
chr10	128059307	128059675	Eya1_peak_418	124	.	8.15836	17.40049	12.46604	243
chr10	110676637	110676790	Eya1_peak_382	124	.	8.15836	17.40049	12.46604	62
chr8	105693810	105693911	Eya1_peak_3829	124	.	7.09690	17.38039	12.45766	38
chr6	113282089	113282216	Eya1_peak_3330	124	.	7.09690	17.38039	12.45766	58
chr4	46992961	46993103	Eya1_peak_2658	124	.	7.09690	17.38039	12.45766	70
chr2	156677010	156677161	Eya1_peak_2338	124	.	7.09690	17.38039	12.45766	93
chr1	90028488	90028604	Eya1_peak_99	124	.	7.09690	17.38039	12.45766	62
chr13	23990956	23991111	Eya1_peak_1059	124	.	7.09690	17.38039	12.45766	85
chr11	82371712	82371850	Eya1_peak_674	124	.	7.09690	17.38039	12.45766	67
chr7	80993064	80993518	Eya1_peak_3532	124	.	9.05185	17.34402	12.42535	294
chr10	90827073	90827171	Eya1_peak_365	123	.	9.35853	17.31731	12.39896	49
chr9	40269711	40269789	Eya1_peak_3920	123	.	9.02417	17.29891	12.38175	38
chr4	63544858	63545351	Eya1_peak_2681	123	.	9.02417	17.29891	12.38175	147
chr17	3115300	3115413	Eya1_peak_1618	123	.	9.02417	17.29891	12.38175	42
chr13	17695529	17695696	Eya1_peak_1038	123	.	9.02417	17.29891	12.38175	103
chr11	81115800	81115945	Eya1_peak_670	123	.	9.29675	17.21804	12.30533	80
chr11	77607492	77607821	Eya1_peak_641	123	.	9.29675	17.21804	12.30533	221
chr8	70352939	70353143	Eya1_peak_3746	122	.	8.96931	17.20944	12.29809	156
chr2	118779677	118779766	Eya1_peak_2263	122	.	8.64114	17.19051	12.27938	60
chr11	78496009	78496134	Eya1_peak_657	122	.	8.64114	17.19051	12.27938	90
chr11	69395849	69396010	Eya1_peak_587	122	.	8.64114	17.19051	12.27938	66
chr5	33820797	33821103	Eya1_peak_2925	122	.	8.94213	17.16508	12.25664	128
chr11	120990565	120991048	Eya1_peak_853	122	.	8.91511	17.12097	12.21316	403
chr4	103875698	103875848	Eya1_peak_2715	121	.	9.20561	17.07150	12.16613	63
chr15	81585528	81585803	Eya1_peak_1432	121	.	9.20561	17.07150	12.16613	168
chr12	70974783	70974991	Eya1_peak_932	121	.	8.86156	17.03346	12.12892	127
chr7	114254302	114254718	Eya1_peak_3583	121	.	9.17562	17.02327	12.11888	71
chr2	43613685	43613824	Eya1_peak_2157	121	.	9.17562	17.02327	12.11888	66
chr18	21001956	21002108	Eya1_peak_1839	121	.	9.17562	17.02327	12.11888	88
chr1	135634944	135635091	Eya1_peak_140	121	.	9.17562	17.02327	12.11888	36
chr11	104053376	104053512	Eya1_peak_777	120	.	9.11623	16.92770	12.02791	72
chr1	181210982	181211214	Eya1_peak_203	119	.	9.08682	16.88036	11.98119	171
chr5	65763280	65763833	Eya1_peak_2964	119	.	8.75638	16.86128	11.96287	69
chr4	124860577	124860745	Eya1_peak_2756	119	.	8.75638	16.86128	11.96287	34
chr18	34777065	34777558	Eya1_peak_1860	119	.	8.75638	16.86128	11.96287	217
chr2	158570515	158570602	Eya1_peak_2353	119	.	7.85213	16.85652	11.96075	38
chr9	121791342	121791495	Eya1_peak_4132	119	.	8.40568	16.79602	11.90165	83
chr2	69897412	69897853	Eya1_peak_2185	119	.	8.40568	16.79602	11.90165	381
chr10	119239112	119239548	Eya1_peak_398	119	.	8.40568	16.79602	11.90165	274
chrX	94122708	94123418	Eya1_peak_4150	118	.	9.34454	16.78158	11.88914	34
chr9	26727583	26727693	Eya1_peak_3912	118	.	9.34454	16.78158	11.88914	68
chr7	51621837	51621946	Eya1_peak_3500	118	.	9.34454	16.78158	11.88914	54
chr7	117021827	117021986	Eya1_peak_3586	118	.	9.34454	16.78158	11.88914	88
chr4	133753529	133753746	Eya1_peak_2808	118	.	8.70472	16.77656	11.88914	49
chr3	16183570	16183691	Eya1_peak_2435	118	.	9.34454	16.78158	11.88914	66
chr19	22139293	22139436	Eya1_peak_2009	118	.	9.34454	16.78158	11.88914	70
chr1	79440002	79440146	Eya1_peak_80	118	.	9.34454	16.78158	11.88914	18
chr17	48917557	48917644	Eya1_peak_1756	118	.	9.34454	16.78158	11.88914	53
chr16	39985141	39985250	Eya1_peak_1571	118	.	9.34454	16.78158	11.88914	47
chr12	106633218	106633338	Eya1_peak_1001	118	.	9.34454	16.78158	11.88914	88
chr12	102949728	102949830	Eya1_peak_995	118	.	9.34454	16.78158	11.88914	64
chr11	66259009	66259091	Eya1_peak_577	118	.	9.34454	16.78158	11.88914	37
chr10	94305644	94305759	Eya1_peak_374	118	.	9.34454	16.78158	11.88914	54
chr10	34282286	34282614	Eya1_peak_248	118	.	9.34454	16.78158	11.88914	71
chr2	163439324	163439404	Eya1_peak_2365	118	.	8.99972	16.74006	11.85498	38
chr2	166995940	166996230	Eya1_peak_2384	118	.	9.31572	16.73557	11.85117	136
chr17	47502085	47502280	Eya1_peak_1752	118	.	8.97106	16.69386	11.81013	107
chr10	91384430	91384516	Eya1_peak_369	118	.	8.97106	16.69386	11.81013	36
chr8	9309608	9309725	Eya1_peak_3684	118	.	9.28348	16.68411	11.80132	65
chr17	42876172	42876330	Eya1_peak_1731	118	.	9.28348	16.68411	11.80132	97
chr2	156111392	156111766	Eya1_peak_2333	117	.	8.94258	16.64793	11.76582	294
chr11	82313250	82313387	Eya1_peak_673	117	.	9.21968	16.58225	11.70153	87
chr7	82625451	82625609	Eya1_peak_3536	116	.	8.88615	16.55691	11.67658	59
chr6	83914707	83914860	Eya1_peak_3292	116	.	8.88615	16.55691	11.67658	83
chr19	12794978	12795064	Eya1_peak_2004	116	.	8.88615	16.55691	11.67658	38
chr9	45710577	45710656	Eya1_peak_3936	116	.	9.18810	16.53184	11.65467	40
chr12	65036330	65036797	Eya1_peak_916	116	.	9.18810	16.53184	11.65467	255
chr11	77930844	77931116	Eya1_peak_646	115	.	8.50402	16.44647	11.57114	72
chr2	26933085	26933311	Eya1_peak_2105	115	.	8.18271	16.41961	11.54750	161
chr4	116075436	116076501	Eya1_peak_2734	115	.	6.85236	16.40859	11.53696	749
chr3	90052011	90052399	Eya1_peak_2499	115	.	6.85236	16.40859	11.53696	168
chr13	54945433	54945584	Eya1_peak_1103	115	.	6.85236	16.40859	11.53696	83
chr11	103656673	103656822	Eya1_peak_775	115	.	6.85236	16.40859	11.53696	60
chr5	146360502	146360631	Eya1_peak_3168	115	.	9.09466	16.38267	11.51420	64
chr17	88064645	88065554	Eya1_peak_1813	115	.	9.09466	16.38267	11.51420	519
chr12	113098409	113098918	Eya1_peak_1021	114	.	8.74816	16.33397	11.46691	341
chr8	8690201	8690526	Eya1_peak_3683	114	.	7.83232	16.31975	11.45305	262
chr7	111081802	111082617	Eya1_peak_3574	114	.	7.83232	16.31975	11.45305	671
chr5	62483689	62483780	Eya1_peak_2954	114	.	7.83232	16.31975	11.45305	39
chr4	44704397	44704585	Eya1_peak_2653	114	.	7.83232	16.31975	11.45305	82
chr3	58576721	58577073	Eya1_peak_2467	114	.	7.83232	16.31975	11.45305	192
chr2	25982729	25983067	Eya1_peak_2100	114	.	7.83232	16.31975	11.45305	70
chr2	152414284	152414517	Eya1_peak_2309	114	.	7.83232	16.31975	11.45305	169
chr17	7741124	7741260	Eya1_peak_1631	114	.	7.83232	16.31975	11.45305	55
chr5	121009542	121009704	Eya1_peak_3069	114	.	9.03341	16.28488	11.43014	59
chr14	73142996	73143427	Eya1_peak_1312	114	.	9.03341	16.28488	11.43014	181
chr10	80748721	80748926	Eya1_peak_335	113	.	8.69416	16.24659	11.39406	114
chr11	32455058	32455319	Eya1_peak_490	113	.	9.00309	16.23647	11.38449	145
chr8	33929426	33929771	Eya1_peak_3716	112	.	8.94307	16.14061	11.29036	188
chr1	84838926	84839180	Eya1_peak_87	112	.	8.94307	16.14061	11.29036	126
chr17	4994503	4994618	Eya1_peak_1622	112	.	8.94307	16.14061	11.29036	55
chr1	63614752	63614856	Eya1_peak_60	112	.	8.94307	16.14061	11.29036	53
chr9	102625719	102625850	Eya1_peak_4064	112	.	8.61440	16.11738	11.26846	46
chr16	8830721	8830969	Eya1_peak_1506	112	.	8.61440	16.11738	11.26846	98
chr12	85339017	85339364	Eya1_peak_969	112	.	8.61440	16.11738	11.26846	234
chr11	58009167	58009458	Eya1_peak_553	112	.	8.61440	16.11738	11.26846	60
chr10	58446881	58447295	Eya1_peak_277	112	.	8.61440	16.11738	11.26846	327
chr12	54862361	54862611	Eya1_peak_904	112	.	8.91336	16.09314	11.24820	174
chr19	45097977	45098097	Eya1_peak_2042	112	.	8.26581	16.05236	11.20937	49
chr15	96287006	96287243	Eya1_peak_1464	112	.	8.88384	16.04598	11.20494	97
chr11	32642853	32643190	Eya1_peak_491	111	.	8.56203	16.03245	11.19274	215
chr11	35769754	35770209	Eya1_peak_501	111	.	8.85452	15.99913	11.15977	170
chr11	20201474	20201943	Eya1_peak_467	111	.	8.85452	15.99913	11.15977	236
chr1	74392026	74392286	Eya1_peak_69	111	.	8.53608	15.99034	11.15266	51
chr6	71271638	71271928	Eya1_peak_3276	110	.	8.79646	15.90631	11.07115	253
chr17	34899043	34899592	Eya1_peak_1705	110	.	8.79646	15.90631	11.07115	201
chr9	113741240	113741388	Eya1_peak_4111	110	.	8.76771	15.86034	11.02677	94
chr7	109129581	109129672	Eya1_peak_3566	109	.	8.73915	15.81466	10.98217	39
chr3	135438984	135439397	Eya1_peak_2566	109	.	8.73915	15.81466	10.98217	105
chr2	91526817	91527208	Eya1_peak_2219	109	.	8.73915	15.81466	10.98217	70
chr17	84958048	84958153	Eya1_peak_1808	109	.	8.73915	15.81466	10.98217	50
chr12	92040610	92040719	Eya1_peak_981	109	.	8.73915	15.81466	10.98217	41
chr11	51263355	51263496	Eya1_peak_524	109	.	8.71077	15.76926	10.94092	83
chr8	19980100	19980287	Eya1_peak_3698	108	.	6.74269	15.72432	10.89659	132
chr10	62791761	62792101	Eya1_peak_290	108	.	7.77047	15.71528	10.88817	218
chr5	116545913	116546006	Eya1_peak_3054	108	.	8.35876	15.70195	10.87493	36
chr1	4857782	4858014	Eya1_peak_2	108	.	8.35876	15.70195	10.87493	130
chr14	47649411	47649798	Eya1_peak_1263	108	.	8.35876	15.70195	10.87493	319
chr14	34673914	34674413	Eya1_peak_1251	108	.	8.35876	15.70195	10.87493	353
chr13	98316480	98316913	Eya1_peak_1172	108	.	8.35876	15.70195	10.87493	148
chr5	88675466	88675669	Eya1_peak_2987	108	.	8.65457	15.67932	10.85590	118
chr1	167187921	167188027	Eya1_peak_183	108	.	8.65457	15.67932	10.85590	47
chr12	80112205	80112568	Eya1_peak_946	108	.	8.04057	15.67711	10.85434	94
chr6	31398837	31399374	Eya1_peak_3208	108	.	8.62674	15.63476	10.81378	251
chr5	147430822	147431249	Eya1_peak_3174	108	.	8.62674	15.63476	10.81378	62
chr5	116554041	116554146	Eya1_peak_3055	108	.	8.62674	15.63476	10.81378	48
chr8	33386049	33386187	Eya1_peak_3712	107	.	8.87783	15.54125	10.72335	51
chr6	8209454	8209590	Eya1_peak_3188	107	.	8.87783	15.54125	10.72335	52
chr4	14145576	14145715	Eya1_peak_2616	107	.	8.87783	15.54125	10.72335	72
chr3	16183292	16183469	Eya1_peak_2434	107	.	8.87783	15.54125	10.72335	77
chr2	94524683	94524781	Eya1_peak_2235	107	.	8.87783	15.54125	10.72335	50
chr17	39129231	39129356	Eya1_peak_1721	107	.	8.87783	15.54125	10.72335	52
chr16	62758479	62758601	Eya1_peak_1586	107	.	8.87783	15.54125	10.72335	58
chr1	3670709	3670908	Eya1_peak_1	107	.	8.87783	15.54125	10.72335	128
chr12	70347180	70347333	Eya1_peak_930	107	.	8.87783	15.54125	10.72335	63
chr12	5717647	5717738	Eya1_peak_865	107	.	8.87783	15.54125	10.72335	46
chr1	159702166	159702307	Eya1_peak_169	107	.	8.87783	15.54125	10.72335	50
chr10	6788819	6788922	Eya1_peak_223	107	.	8.87783	15.54125	10.72335	59
chr4	151995612	151995908	Eya1_peak_2868	106	.	8.54432	15.50271	10.69313	246
chr11	57434298	57434411	Eya1_peak_551	106	.	8.85045	15.49779	10.68930	42
chr8	105496924	105497056	Eya1_peak_3825	106	.	8.51719	15.45923	10.65137	93
chr17	46383835	46383943	Eya1_peak_1742	106	.	8.51719	15.45923	10.65137	46
chr11	84944041	84944219	Eya1_peak_685	106	.	8.51719	15.45923	10.65137	65
chr6	33126717	33126854	Eya1_peak_3213	106	.	6.60783	15.45244	10.64507	54
chr2	24762018	24762151	Eya1_peak_2092	106	.	6.60783	15.45244	10.64507	78
chr17	25273508	25274020	Eya1_peak_1655	106	.	6.60783	15.45244	10.64507	209
chr17	25272890	25273340	Eya1_peak_1654	106	.	6.60783	15.45244	10.64507	308
chr13	58402234	58402449	Eya1_peak_1130	106	.	6.60783	15.45244	10.64507	97
chr7	120426818	120426891	Eya1_peak_3594	106	.	8.81983	15.44919	10.64485	25
chr15	87887164	87887242	Eya1_peak_1450	106	.	8.81983	15.44919	10.64485	28
chr12	104751342	104751762	Eya1_peak_996	106	.	8.49024	15.41600	10.61249	348
chr6	52713754	52714160	Eya1_peak_3267	105	.	8.46345	15.37303	10.57051	315
chr2	18064653	18064972	Eya1_peak_2079	105	.	8.75921	15.35299	10.55392	209
chr17	63499463	63500102	Eya1_peak_1768	105	.	8.75921	15.35299	10.55392	543
chr16	9836669	9836762	Eya1_peak_1508	105	.	8.75921	15.35299	10.55392	62
chr11	21238849	21239621	Eya1_peak_475	105	.	8.43684	15.33032	10.53203	65
chr3	103573908	103574051	Eya1_peak_2533	105	.	7.82729	15.31911	10.52166	42
chr15	76477536	76477660	Eya1_peak_1401	105	.	7.82729	15.31911	10.52166	65
chr3	8508196	8508289	Eya1_peak_2428	105	.	8.11787	15.30826	10.51147	35
chr2	180920570	180920714	Eya1_peak_2421	105	.	8.11787	15.30826	10.51147	50
chr19	8820233	8820597	Eya1_peak_1992	105	.	8.72921	15.30538	10.51147	258
chr12	86994360	86994448	Eya1_peak_974	105	.	8.11787	15.30826	10.51147	45
chr11	52232093	52232236	Eya1_peak_533	105	.	8.11787	15.30826	10.51147	95
chr8	46740768	46741019	Eya1_peak_3727	104	.	8.41039	15.28786	10.49512	92
chr7	120917895	120918344	Eya1_peak_3596	104	.	8.69941	15.25811	10.46585	114
chr4	62257084	62257219	Eya1_peak_2677	104	.	8.69941	15.25811	10.46585	44
chr9	72662458	72663089	Eya1_peak_4020	104	.	7.50627	15.25735	10.46552	459
chr9	119706827	119706971	Eya1_peak_4124	104	.	7.50627	15.25735	10.46552	61
chr8	71671663	71671813	Eya1_peak_3752	104	.	7.50627	15.25735	10.46552	49
chr7	25754078	25754770	Eya1_peak_3439	104	.	7.50627	15.25735	10.46552	485
chr7	16183792	16183984	Eya1_peak_3411	104	.	7.50627	15.25735	10.46552	116
chr6	29735700	29736347	Eya1_peak_3201	104	.	7.50627	15.25735	10.46552	340
chr5	113716718	113716909	Eya1_peak_3037	104	.	7.50627	15.25735	10.46552	59
chr4	117893529	117893660	Eya1_peak_2739	104	.	7.50627	15.25735	10.46552	63
chr3	51416159	51416724	Eya1_peak_2459	104	.	7.50627	15.25735	10.46552	454
chr2	154892374	154892729	Eya1_peak_2321	104	.	7.50627	15.25735	10.46552	193
chr2	109675985	109676095	Eya1_peak_2249	104	.	7.50627	15.25735	10.46552	58
chr19	42397410	42397579	Eya1_peak_2035	104	.	7.50627	15.25735	10.46552	91
chr19	37207649	37208143	Eya1_peak_2024	104	.	7.50627	15.25735	10.46552	198
chr1	93272616	93272762	Eya1_peak_103	104	.	7.50627	15.25735	10.46552	91
chr14	75366893	75367015	Eya1_peak_1314	104	.	7.50627	15.25735	10.46552	62
chr13	42711668	42711814	Eya1_peak_1080	104	.	7.50627	15.25735	10.46552	76
chr13	105442714	105442844	Eya1_peak_1184	104	.	7.50627	15.25735	10.46552	65
chr11	12025851	12026021	Eya1_peak_461	104	.	7.50627	15.25735	10.46552	45
chr11	103132311	103132684	Eya1_peak_774	104	.	7.50627	15.25735	10.46552	305
chr10	81477668	81477831	Eya1_peak_348	104	.	7.50627	15.25735	10.46552	50
chr10	76958348	76958430	Eya1_peak_306	104	.	7.50627	15.25735	10.46552	34
chr16	20517215	20517397	Eya1_peak_1538	104	.	8.38411	15.24564	10.46501	93
chr9	108517096	108517263	Eya1_peak_4093	104	.	8.66982	15.21115	10.43159	127
chr11	84724269	84724380	Eya1_peak_681	104	.	8.66982	15.21115	10.43159	62
chr8	95806773	95807075	Eya1_peak_3813	103	.	8.33203	15.16196	10.38554	228
chr7	44593893	44594090	Eya1_peak_3483	103	.	5.87314	15.16215	10.38554	117
chr14	68125671	68125796	Eya1_peak_1306	103	.	5.87314	15.16215	10.38554	61
chr16	8737936	8738395	Eya1_peak_1503	103	.	8.61124	15.11818	10.34302	27
chr1	159524227	159524358	Eya1_peak_167	103	.	8.61124	15.11818	10.34302	62
chr11	96005522	96005855	Eya1_peak_724	103	.	8.28059	15.07923	10.30452	63
chr11	118659410	118659517	Eya1_peak_834	103	.	8.28059	15.07923	10.30452	72
chr9	98234883	98234980	Eya1_peak_4053	102	.	8.58224	15.07216	10.29779	37
chr4	8535721	8535997	Eya1_peak_2606	102	.	8.58224	15.07216	10.29779	204
chr16	5765282	5765409	Eya1_peak_1500	102	.	8.58224	15.07216	10.29779	72
chr11	106084637	106085384	Eya1_peak_786	102	.	8.58224	15.07216	10.29779	52
chr15	76351434	76351512	Eya1_peak_1400	102	.	7.39777	15.06764	10.29579	28
chr7	30346761	30346943	Eya1_peak_3457	102	.	8.55344	15.02645	10.25587	55
chr17	6490667	6490839	Eya1_peak_1630	102	.	7.64478	15.01049	10.24059	116
chr4	123664106	123664436	Eya1_peak_2748	102	.	8.22979	14.99745	10.22758	261
chr8	78508485	78508893	Eya1_peak_3761	102	.	7.62502	14.97695	10.20832	67
chr5	35299759	35299877	Eya1_peak_2933	102	.	7.62502	14.97695	10.20832	55
chr8	95028537	95028634	Eya1_peak_3811	101	.	8.20462	14.95691	10.18869	46
chr6	32710303	32710467	Eya1_peak_3212	101	.	8.20462	14.95691	10.18869	63
chr6	117908047	117908287	Eya1_peak_3350	101	.	8.20462	14.95691	10.18869	34
chr14	62760578	62760815	Eya1_peak_1294	101	.	8.20462	14.95691	10.18869	49
chr12	87471904	87472212	Eya1_peak_977	101	.	8.20462	14.95691	10.18869	220
chr11	98324122	98324254	Eya1_peak_745	101	.	8.20462	14.95691	10.18869	77
chr11	4750371	4750579	Eya1_peak_446	101	.	8.20462	14.95691	10.18869	54
chr10	11081594	11081712	Eya1_peak_234	101	.	8.20462	14.95691	10.18869	66
chr4	99194016	99194120	Eya1_peak_2704	101	.	7.89047	14.93427	10.17177	54
chr16	8830189	8830643	Eya1_peak_1505	101	.	7.89047	14.93427	10.17177	113
chr17	29614921	29615084	Eya1_peak_1680	101	.	8.46819	14.89111	10.13131	58
chr14	66909853	66909969	Eya1_peak_1305	101	.	8.46819	14.89111	10.13131	50
chr7	123503469	123503594	Eya1_peak_3608	100	.	8.44015	14.84658	10.08846	55
chr5	115429751	115430116	Eya1_peak_3046	100	.	8.44015	14.84658	10.08846	216
chr4	86748804	86749234	Eya1_peak_2690	100	.	8.44015	14.84658	10.08846	183
chr4	46451555	46452189	Eya1_peak_2656	100	.	8.13003	14.83664	10.07938	412
chr5	44226847	44227098	Eya1_peak_2947	100	.	8.10547	14.79700	10.04169	157
chr16	23107825	23107987	Eya1_peak_1547	100	.	8.10547	14.79700	10.04169	53
chr15	82921205	82921352	Eya1_peak_1436	100	.	8.10547	14.79700	10.04169	113
chr7	45216116	45216230	Eya1_peak_3491	100	.	8.08105	14.75757	10.00387	63
chr5	148070074	148070179	Eya1_peak_3175	100	.	8.38462	14.75838	10.00387	50
chr10	42761653	42762124	Eya1_peak_262	100	.	8.38462	14.75838	10.00387	344
chr4	123664574	123664700	Eya1_peak_2749	99	.	8.05678	14.71837	9.96534	35
chr18	61555400	61555923	Eya1_peak_1901	99	.	8.03266	14.67938	9.92753	257
chr9	72532543	72532694	Eya1_peak_4019	99	.	8.32981	14.67130	9.91958	56
chr12	3807921	3808058	Eya1_peak_860	99	.	8.32981	14.67130	9.91958	96
chr1	127774305	127774661	Eya1_peak_117	99	.	8.32981	14.67130	9.91958	198
chr8	79398852	79398963	Eya1_peak_3766	98	.	8.30268	14.62818	9.87771	60
chr5	112575575	112575710	Eya1_peak_3031	98	.	8.30268	14.62818	9.87771	64
chr3	146812637	146812898	Eya1_peak_2585	98	.	8.30268	14.62818	9.87771	103
chr19	3767624	3767729	Eya1_peak_1946	98	.	8.30268	14.62818	9.87771	40
chr16	23890281	23890385	Eya1_peak_1548	98	.	8.30268	14.62818	9.87771	55
chr1	55027097	55027348	Eya1_peak_40	98	.	8.30268	14.62818	9.87771	179
chr14	34502915	34503100	Eya1_peak_1249	98	.	8.30268	14.62818	9.87771	56
chr13	14613291	14613662	Eya1_peak_1036	98	.	8.30268	14.62818	9.87771	52
chr11	58009527	58009873	Eya1_peak_554	98	.	8.30268	14.62818	9.87771	195
chr11	23307064	23307204	Eya1_peak_480	98	.	8.30268	14.62818	9.87771	39
chr9	21546938	21547136	Eya1_peak_3904	98	.	8.27572	14.58532	9.83922	44
chr7	3645651	3645829	Eya1_peak_3392	98	.	8.27572	14.58532	9.83922	37
chr7	127614997	127615257	Eya1_peak_3635	98	.	8.27572	14.58532	9.83922	99
chr8	3279402	3279522	Eya1_peak_3677	98	.	7.67546	14.57825	9.83308	67
chr2	31759994	31760349	Eya1_peak_2128	98	.	7.67546	14.57825	9.83308	265
chr19	45659796	45660362	Eya1_peak_2043	98	.	7.67546	14.57825	9.83308	354
chr6	48086118	48086480	Eya1_peak_3246	98	.	7.96115	14.56367	9.82017	99
chr5	27366082	27366208	Eya1_peak_2904	98	.	7.96115	14.56367	9.82017	48
chr5	117264875	117264980	Eya1_peak_3060	98	.	7.96115	14.56367	9.82017	53
chr5	116829931	116830089	Eya1_peak_3058	98	.	7.96115	14.56367	9.82017	41
chr4	44434730	44434828	Eya1_peak_2650	98	.	7.96115	14.56367	9.82017	55
chr17	24550113	24550460	Eya1_peak_1649	98	.	7.96115	14.56367	9.82017	124
chr6	83927572	83927689	Eya1_peak_3293	97	.	6.36330	14.51252	9.77333	66
chr14	50720002	50720159	Eya1_peak_1269	97	.	6.36330	14.51252	9.77333	106
chr12	84698611	84698781	Eya1_peak_965	97	.	6.36330	14.51252	9.77333	72
chr11	55897637	55897811	Eya1_peak_549	97	.	6.36330	14.51252	9.77333	62
chr10	71428393	71428502	Eya1_peak_301	97	.	6.36330	14.51252	9.77333	43
chr15	84109066	84109254	Eya1_peak_1441	97	.	8.22233	14.50041	9.76486	33
chr2	165160594	165160713	Eya1_peak_2379	97	.	8.19589	14.45834	9.72388	39
chr19	42326040	42326167	Eya1_peak_2034	97	.	8.19589	14.45834	9.72388	58
chr15	12118467	12118725	Eya1_peak_1351	97	.	8.19589	14.45834	9.72388	26
chr13	55714733	55714869	Eya1_peak_1117	96	.	8.16962	14.41654	9.68337	86
chr7	116093352	116093611	Eya1_peak_3585	96	.	8.14352	14.37499	9.64277	165
chr4	133752611	133753045	Eya1_peak_2805	96	.	7.84476	14.37492	9.64277	40
chr18	73572878	73573418	Eya1_peak_1914	96	.	8.14352	14.37499	9.64277	433
chr11	116852169	116852251	Eya1_peak_824	96	.	8.14352	14.37499	9.64277	23
chr4	151185895	151185986	Eya1_peak_2860	96	.	7.25032	14.33534	9.60425	41
chr9	52168033	52168537	Eya1_peak_3950	96	.	8.11758	14.33369	9.60280	448
chr10	117375918	117376429	Eya1_peak_394	96	.	8.11758	14.33369	9.60280	391
chr7	124742213	124742340	Eya1_peak_3610	95	.	8.41113	14.32425	9.59446	60
chr4	44260459	44260599	Eya1_peak_2649	95	.	8.41113	14.32425	9.59446	87
chr4	3835260	3835617	Eya1_peak_2600	95	.	8.41113	14.32425	9.59446	177
chr2	165687656	165687746	Eya1_peak_2381	95	.	8.41113	14.32425	9.59446	41
chr2	162031748	162031852	Eya1_peak_2360	95	.	8.41113	14.32425	9.59446	46
chr19	21272999	21273084	Eya1_peak_2008	95	.	8.41113	14.32425	9.59446	46
chr18	6765430	6765592	Eya1_peak_1823	95	.	8.41113	14.32425	9.59446	94
chr15	101879892	101880025	Eya1_peak_1487	95	.	8.41113	14.32425	9.59446	52
chr12	105785065	105785199	Eya1_peak_999	95	.	8.41113	14.32425	9.59446	65
chr9	119149701	119149869	Eya1_peak_4119	95	.	5.67752	14.29954	9.57879	71
chr5	116591454	116591613	Eya1_peak_3056	95	.	5.67752	14.29954	9.57879	68
chr5	65537749	65537982	Eya1_peak_2962	95	.	8.09181	14.29264	9.57239	47
chr5	108694508	108694603	Eya1_peak_3021	95	.	8.09181	14.29264	9.57239	60
chr3	27370242	27370442	Eya1_peak_2440	95	.	8.09181	14.29264	9.57239	114
chr12	8674445	8674843	Eya1_peak_868	95	.	8.09181	14.29264	9.57239	147
chr8	105636947	105637176	Eya1_peak_3828	95	.	8.06620	14.25184	9.53325	203
chr9	110116953	110117364	Eya1_peak_4102	95	.	7.47186	14.23865	9.52050	223
chr5	142694732	142694862	Eya1_peak_3153	95	.	7.47186	14.23865	9.52050	89
chr13	111687109	111687234	Eya1_peak_1192	95	.	8.35617	14.23760	9.52017	61
chr9	61373039	61373135	Eya1_peak_3987	94	.	7.18023	14.21410	9.49742	30
chr9	46980283	46980372	Eya1_peak_3941	94	.	7.18023	14.21410	9.49742	40
chr7	28505735	28505819	Eya1_peak_3450	94	.	7.18023	14.21410	9.49742	32
chr7	12478390	12478871	Eya1_peak_3404	94	.	7.18023	14.21410	9.49742	158
chr6	113962914	113963004	Eya1_peak_3337	94	.	7.18023	14.21410	9.49742	52
chr5	65697118	65697760	Eya1_peak_2963	94	.	7.18023	14.21410	9.49742	114
chr5	37257373	37257507	Eya1_peak_2941	94	.	7.18023	14.21410	9.49742	63
chr5	142906154	142906701	Eya1_peak_3157	94	.	7.18023	14.21410	9.49742	276
chr5	129287599	129287710	Eya1_peak_3110	94	.	8.04075	14.21128	9.49742	59
chr5	122264129	122264407	Eya1_peak_3079	94	.	7.18023	14.21410	9.49742	149
chr5	115272343	115272653	Eya1_peak_3045	94	.	7.18023	14.21410	9.49742	239
chr4	138325837	138326036	Eya1_peak_2831	94	.	7.18023	14.21410	9.49742	83
chr4	132308767	132308956	Eya1_peak_2799	94	.	7.18023	14.21410	9.49742	125
chr3	55112166	55112349	Eya1_peak_2461	94	.	8.04075	14.21128	9.49742	54
chr3	135438801	135438909	Eya1_peak_2565	94	.	8.04075	14.21128	9.49742	46
chr2	178735197	178735363	Eya1_peak_2406	94	.	8.04075	14.21128	9.49742	63
chr1	99772342	99772459	Eya1_peak_108	94	.	7.18023	14.21410	9.49742	47
chr18	76853220	76853304	Eya1_peak_1925	94	.	7.18023	14.21410	9.49742	15
chr17	37046227	37046347	Eya1_peak_1719	94	.	7.18023	14.21410	9.49742	53
chr17	30005167	30005259	Eya1_peak_1682	94	.	8.04075	14.21128	9.49742	35
chr16	18288859	18289209	Eya1_peak_1533	94	.	8.04075	14.21128	9.49742	68
chr15	102670791	102670985	Eya1_peak_1493	94	.	7.18023	14.21410	9.49742	55
chr1	5022813	5022938	Eya1_peak_4	94	.	7.18023	14.21410	9.49742	59
chr13	98925692	98926645	Eya1_peak_1173	94	.	7.18023	14.21410	9.49742	372
chr13	58663435	58663596	Eya1_peak_1131	94	.	7.18023	14.21410	9.49742	97
chr13	34875606	34875946	Eya1_peak_1072	94	.	8.04075	14.21128	9.49742	127
chr11	94321458	94321749	Eya1_peak_713	94	.	7.18023	14.21410	9.49742	237
chr1	176697237	176697317	Eya1_peak_189	94	.	7.18023	14.21410	9.49742	31
chr1	17145551	17145678	Eya1_peak_14	94	.	7.18023	14.21410	9.49742	59
chr11	69671974	69672214	Eya1_peak_590	94	.	8.04075	14.21128	9.49742	97
chr11	104114853	104114970	Eya1_peak_778	94	.	7.18023	14.21410	9.49742	49
chr11	102184781	102184881	Eya1_peak_762	94	.	7.18023	14.21410	9.49742	29
chr10	45546997	45547078	Eya1_peak_268	94	.	7.18023	14.21410	9.49742	34
chr10	128083331	128083762	Eya1_peak_419	94	.	7.18023	14.21410	9.49742	135
chr4	128727690	128728021	Eya1_peak_2776	94	.	8.32736	14.19217	9.49134	261
chr4	101550800	101550881	Eya1_peak_2709	94	.	8.32736	14.19217	9.49134	58
chr15	86544202	86544369	Eya1_peak_1448	94	.	8.32736	14.19217	9.49134	47
chr8	13339019	13339293	Eya1_peak_3695	94	.	7.73171	14.19107	9.49076	232
chr7	10325757	10325837	Eya1_peak_3403	94	.	7.73171	14.19107	9.49076	53
chr4	87221697	87221826	Eya1_peak_2692	94	.	7.73171	14.19107	9.49076	59
chr14	26970310	26970434	Eya1_peak_1226	94	.	7.73171	14.19107	9.49076	64
chr11	97279886	97280535	Eya1_peak_732	94	.	8.01547	14.17096	9.47363	525
chr10	81136954	81137158	Eya1_peak_342	94	.	7.68740	14.11886	9.42402	38
chr3	80802944	80803070	Eya1_peak_2481	94	.	8.27032	14.10225	9.40771	48
chr11	78165132	78165323	Eya1_peak_653	93	.	7.96537	14.09104	9.39697	65
chr2	125858693	125858923	Eya1_peak_2279	93	.	8.24209	14.05775	9.36464	64
chr4	152424499	152424609	Eya1_peak_2871	93	.	7.94055	14.05143	9.35918	53
chr2	73910675	73910993	Eya1_peak_2195	93	.	7.94055	14.05143	9.35918	195
chr15	98871209	98871374	Eya1_peak_1479	93	.	7.94055	14.05143	9.35918	119
chr11	98795776	98796170	Eya1_peak_750	93	.	7.94055	14.05143	9.35918	270
chr14	104453991	104454087	Eya1_peak_1334	93	.	8.21405	14.01356	9.32344	36
chr5	148928812	148928938	Eya1_peak_3178	93	.	7.91589	14.01206	9.32283	63
chr13	94976389	94976594	Eya1_peak_1169	92	.	7.89138	13.97291	9.28429	39
chr2	32151274	32151542	Eya1_peak_2130	92	.	7.86703	13.93398	9.24690	203
chr19	5801116	5801388	Eya1_peak_1972	92	.	7.86703	13.93398	9.24690	99
chr16	20619983	20620081	Eya1_peak_1540	92	.	8.15855	13.92607	9.23962	32
chr3	130060421	130060620	Eya1_peak_2564	92	.	7.27878	13.91415	9.22865	44
chr5	108549640	108549747	Eya1_peak_3020	91	.	8.13108	13.88277	9.19855	43
chr19	41263723	41263998	Eya1_peak_2028	91	.	8.13108	13.88277	9.19855	43
chr1	58423732	58423886	Eya1_peak_48	91	.	8.13108	13.88277	9.19855	14
chr13	54260412	54260488	Eya1_peak_1095	91	.	8.13108	13.88277	9.19855	40
chr12	108178806	108179249	Eya1_peak_1003	91	.	8.13108	13.88277	9.19855	380
chr10	125966795	125966869	Eya1_peak_408	91	.	8.13108	13.88277	9.19855	24
chr6	47748613	47748855	Eya1_peak_3238	91	.	3.75131	13.87458	9.19366	181
chr10	5639265	5639357	Eya1_peak_221	91	.	8.10379	13.83975	9.15938	54
chr5	112824518	112824644	Eya1_peak_3033	91	.	7.51513	13.83721	9.15770	61
chr4	155812626	155812839	Eya1_peak_2884	91	.	7.51513	13.83721	9.15770	48
chr1	131910547	131910688	Eya1_peak_122	91	.	7.51513	13.83721	9.15770	78
chr9	119389101	119389237	Eya1_peak_4120	91	.	7.79485	13.81854	9.14080	60
chr8	91313531	91313763	Eya1_peak_3800	91	.	7.79485	13.81854	9.14080	92
chr8	84969988	84970085	Eya1_peak_3783	91	.	7.79485	13.81854	9.14080	57
chr6	28423754	28424002	Eya1_peak_3199	91	.	7.79485	13.81854	9.14080	99
chr4	108780054	108780347	Eya1_peak_2725	91	.	7.79485	13.81854	9.14080	70
chr2	92671844	92671931	Eya1_peak_2228	91	.	7.79485	13.81854	9.14080	35
chr15	81745500	81745748	Eya1_peak_1434	91	.	7.79485	13.81854	9.14080	18
chr11	3774704	3774885	Eya1_peak_442	91	.	7.79485	13.81854	9.14080	113
chr4	115887033	115887108	Eya1_peak_2733	90	.	7.74746	13.74267	9.07146	41
chr15	96288333	96288798	Eya1_peak_1468	90	.	8.02302	13.71240	9.04152	41
chr5	108461550	108461785	Eya1_peak_3019	90	.	7.99645	13.67050	9.00087	132
chr4	154466461	154466552	Eya1_peak_2878	90	.	7.99645	13.67050	9.00087	25
chr5	129725100	129725434	Eya1_peak_3111	89	.	7.97006	13.62887	8.96126	101
chr2	155692048	155692197	Eya1_peak_2330	89	.	7.97006	13.62887	8.96126	46
chr17	74528676	74528914	Eya1_peak_1792	89	.	7.97006	13.62887	8.96126	191
chr4	126255818	126255937	Eya1_peak_2764	89	.	7.09543	13.60354	8.93701	87
chr3	107695942	107696050	Eya1_peak_2545	89	.	7.09543	13.60354	8.93701	63
chr11	98027006	98027104	Eya1_peak_739	89	.	7.09543	13.60354	8.93701	32
chr16	91011566	91011667	Eya1_peak_1599	89	.	7.65440	13.59345	8.92758	54
chr9	57468141	57468242	Eya1_peak_3967	89	.	6.11877	13.58947	8.92401	63
chr7	34702894	34703009	Eya1_peak_3470	89	.	6.11877	13.58947	8.92401	55
chr19	5087879	5088094	Eya1_peak_1957	89	.	6.11877	13.58947	8.92401	156
chr5	24357559	24357689	Eya1_peak_2895	88	.	5.05731	13.55013	8.88988	60
chr9	61914179	61914432	Eya1_peak_3989	88	.	7.91779	13.54641	8.88630	57
chr6	85498317	85498404	Eya1_peak_3298	88	.	7.91779	13.54641	8.88630	44
chr11	44519028	44519137	Eya1_peak_507	88	.	7.91779	13.54641	8.88630	39
chr5	33275343	33275423	Eya1_peak_2923	88	.	7.89192	13.50558	8.84671	62
chr15	96287875	96288071	Eya1_peak_1466	88	.	7.89192	13.50558	8.84671	138
chr1	37299945	37300177	Eya1_peak_27	88	.	7.89192	13.50558	8.84671	165
chr4	12140336	12140462	Eya1_peak_2613	88	.	7.31035	13.50040	8.84253	77
chr8	57652377	57652569	Eya1_peak_3740	88	.	7.86621	13.46501	8.80860	83
chr8	57652205	57652323	Eya1_peak_3739	88	.	7.86621	13.46501	8.80860	78
chr5	137510568	137510718	Eya1_peak_3139	88	.	7.86621	13.46501	8.80860	34
chr5	130363920	130364012	Eya1_peak_3115	88	.	7.86621	13.46501	8.80860	44
chr17	69417396	69417616	Eya1_peak_1780	88	.	7.86621	13.46501	8.80860	176
chr16	17722676	17722907	Eya1_peak_1528	88	.	7.86621	13.46501	8.80860	207
chr12	101083008	101083211	Eya1_peak_989	88	.	7.86621	13.46501	8.80860	145
chr11	49846978	49847073	Eya1_peak_517	88	.	7.86621	13.46501	8.80860	32
chr11	36396432	36396567	Eya1_peak_504	88	.	7.86621	13.46501	8.80860	35
chr7	126949897	126950109	Eya1_peak_3620	87	.	5.48189	13.45200	8.79980	152
chr6	115178977	115179091	Eya1_peak_3339	87	.	5.48189	13.45200	8.79980	49
chr18	46525487	46525617	Eya1_peak_1886	87	.	7.56354	13.44748	8.79606	34
chr17	33760031	33760247	Eya1_peak_1693	87	.	7.56354	13.44748	8.79606	94
chr14	80157117	80157246	Eya1_peak_1325	87	.	7.56354	13.44748	8.79606	110
chr11	86544481	86544658	Eya1_peak_693	87	.	7.56354	13.44748	8.79606	107
chr11	77982944	77983382	Eya1_peak_647	87	.	7.56354	13.44748	8.79606	238
chr11	72607476	72607576	Eya1_peak_614	87	.	7.56354	13.44748	8.79606	48
chr11	107817340	107817443	Eya1_peak_802	87	.	7.56354	13.44748	8.79606	38
chr10	119239630	119239984	Eya1_peak_399	87	.	7.56354	13.44748	8.79606	112
chr11	62456770	62457118	Eya1_peak_573	87	.	7.84067	13.42469	8.77607	174
chr10	95563588	95563688	Eya1_peak_377	87	.	7.84067	13.42469	8.77607	40
chr6	134566464	134566690	Eya1_peak_3379	87	.	7.81529	13.38462	8.73728	156
chr14	122107132	122107474	Eya1_peak_1344	87	.	7.81529	13.38462	8.73728	219
chr1	134560615	134561030	Eya1_peak_132	87	.	7.81529	13.38462	8.73728	59
chr11	104468797	104469403	Eya1_peak_781	87	.	7.81529	13.38462	8.73728	335
chr10	61783434	61783637	Eya1_peak_283	87	.	7.81529	13.38462	8.73728	133
chr6	92091522	92091630	Eya1_peak_3318	86	.	7.79008	13.34480	8.69828	61
chr1	82839821	82840081	Eya1_peak_85	86	.	7.79008	13.34480	8.69828	114
chr6	47454213	47454344	Eya1_peak_3227	86	.	7.74014	13.26590	8.62225	99
chr5	31193310	31193714	Eya1_peak_2912	86	.	7.74014	13.26590	8.62225	162
chr13	94878448	94878525	Eya1_peak_1168	85	.	7.71541	13.22682	8.58422	33
chr10	81378075	81378148	Eya1_peak_346	85	.	7.71541	13.22682	8.58422	26
chr5	122501639	122501738	Eya1_peak_3080	85	.	7.40962	13.19949	8.55762	45
chr9	71485324	71485875	Eya1_peak_4014	85	.	6.85419	13.19086	8.54902	458
chr9	64340595	64341230	Eya1_peak_3999	85	.	6.85419	13.19086	8.54902	159
chr9	122701895	122702022	Eya1_peak_4135	85	.	6.85419	13.19086	8.54902	64
chr9	107381812	107381945	Eya1_peak_4082	85	.	6.85419	13.19086	8.54902	71
chr8	87087610	87087685	Eya1_peak_3792	85	.	6.85419	13.19086	8.54902	49
chr8	123891458	123891548	Eya1_peak_3875	85	.	7.69084	13.18797	8.54902	58
chr6	28982516	28982671	Eya1_peak_3200	85	.	6.85419	13.19086	8.54902	108
chr6	124740850	124741000	Eya1_peak_3363	85	.	6.85419	13.19086	8.54902	91
chr5	128879279	128879376	Eya1_peak_3107	85	.	7.11644	13.17920	8.54902	49
chr4	155018791	155018938	Eya1_peak_2879	85	.	6.85419	13.19086	8.54902	22
chr4	129335168	129335255	Eya1_peak_2781	85	.	7.11644	13.17920	8.54902	20
chr3	158036361	158036563	Eya1_peak_2599	85	.	6.85419	13.19086	8.54902	68
chr3	154819850	154819959	Eya1_peak_2596	85	.	6.85419	13.19086	8.54902	58
chr2	90917501	90917808	Eya1_peak_2216	85	.	6.85419	13.19086	8.54902	163
chr2	48948892	48949191	Eya1_peak_2161	85	.	6.85419	13.19086	8.54902	184
chr2	163564807	163564883	Eya1_peak_2366	85	.	6.85419	13.19086	8.54902	32
chr2	160646116	160646866	Eya1_peak_2356	85	.	6.85419	13.19086	8.54902	272
chr2	130178906	130179253	Eya1_peak_2291	85	.	6.85419	13.19086	8.54902	173
chr19	60790326	60790511	Eya1_peak_2069	85	.	6.85419	13.19086	8.54902	125
chr1	84696318	84696436	Eya1_peak_86	85	.	6.85419	13.19086	8.54902	46
chr18	32163220	32163485	Eya1_peak_1853	85	.	6.85419	13.19086	8.54902	187
chr16	22265486	22265895	Eya1_peak_1546	85	.	6.85419	13.19086	8.54902	223
chr14	57889785	57890119	Eya1_peak_1291	85	.	6.85419	13.19086	8.54902	280
chr14	49525312	49525385	Eya1_peak_1268	85	.	6.85419	13.19086	8.54902	17
chr13	55211971	55212393	Eya1_peak_1108	85	.	6.85419	13.19086	8.54902	212
chr12	116485647	116485807	Eya1_peak_1025	85	.	6.85419	13.19086	8.54902	79
chr1	193036043	193036249	Eya1_peak_216	85	.	6.85419	13.19086	8.54902	117
chr1	192457671	192457793	Eya1_peak_214	85	.	6.85419	13.19086	8.54902	53
chr11	80613653	80613756	Eya1_peak_668	85	.	6.85419	13.19086	8.54902	63
chr11	54303182	54303314	Eya1_peak_540	85	.	6.85419	13.19086	8.54902	73
chr11	50291717	50292169	Eya1_peak_520	85	.	6.85419	13.19086	8.54902	285
chr8	117173844	117173919	Eya1_peak_3854	85	.	7.66643	13.14936	8.52183	26
chr5	135077664	135078172	Eya1_peak_3120	85	.	7.66643	13.14936	8.52183	409
chr9	82975081	82975497	Eya1_peak_4035	85	.	7.94442	13.13190	8.50554	227
chr8	93748861	93748947	Eya1_peak_3802	85	.	7.94442	13.13190	8.50554	38
chr4	47353297	47353482	Eya1_peak_2659	85	.	7.94442	13.13190	8.50554	63
chr3	119783116	119783247	Eya1_peak_2556	85	.	7.94442	13.13190	8.50554	59
chr19	38558972	38559076	Eya1_peak_2025	85	.	7.94442	13.13190	8.50554	42
chr19	23273487	23273739	Eya1_peak_2010	85	.	7.94442	13.13190	8.50554	59
chr18	31609702	31609821	Eya1_peak_1848	85	.	7.94442	13.13190	8.50554	57
chr1	59913093	59913286	Eya1_peak_56	85	.	7.94442	13.13190	8.50554	133
chr15	74382668	74382810	Eya1_peak_1398	85	.	7.94442	13.13190	8.50554	75
chr1	35017600	35017692	Eya1_peak_22	85	.	7.94442	13.13190	8.50554	40
chr12	29465326	29465463	Eya1_peak_885	85	.	7.94442	13.13190	8.50554	84
chr11	34448045	34448189	Eya1_peak_500	85	.	7.94442	13.13190	8.50554	58
chr11	29547432	29547779	Eya1_peak_483	85	.	7.94442	13.13190	8.50554	208
chr16	17891363	17891585	Eya1_peak_1531	84	.	7.64216	13.11098	8.49328	35
chr11	74723532	74723803	Eya1_peak_621	84	.	7.64216	13.11098	8.49328	113
chr11	69996368	69996918	Eya1_peak_600	84	.	7.64216	13.11098	8.49328	313
chr7	97579974	97580121	Eya1_peak_3546	84	.	7.91992	13.09354	8.47873	51
chr2	60125184	60125318	Eya1_peak_2175	84	.	7.34556	13.09598	8.47873	31
chr19	21272683	21272927	Eya1_peak_2007	84	.	7.91992	13.09354	8.47873	191
chr11	77687053	77687192	Eya1_peak_643	84	.	7.34556	13.09598	8.47873	96
chr11	72494157	72494244	Eya1_peak_612	84	.	7.34556	13.09598	8.47873	30
chr1	16519429	16519505	Eya1_peak_12	84	.	7.91992	13.09354	8.47873	31
chr8	72135396	72135757	Eya1_peak_3753	84	.	7.61805	13.07283	8.45909	16
chr8	109737419	109737675	Eya1_peak_3842	84	.	7.61805	13.07283	8.45909	68
chr7	124989614	124989700	Eya1_peak_3611	84	.	7.61805	13.07283	8.45909	41
chr5	88721343	88721472	Eya1_peak_2990	84	.	7.61805	13.07283	8.45909	86
chr5	140218058	140218151	Eya1_peak_3150	84	.	7.61805	13.07283	8.45909	47
chr4	33248417	33248511	Eya1_peak_2627	84	.	7.61805	13.07283	8.45909	34
chr4	103214732	103214988	Eya1_peak_2712	84	.	7.61805	13.07283	8.45909	107
chr2	112379250	112379454	Eya1_peak_2253	84	.	7.61805	13.07283	8.45909	57
chr18	31759619	31759757	Eya1_peak_1850	84	.	7.61805	13.07283	8.45909	72
chr17	66101293	66101408	Eya1_peak_1776	84	.	7.61805	13.07283	8.45909	60
chr17	28621900	28622037	Eya1_peak_1672	84	.	7.61805	13.07283	8.45909	79
chr16	96127297	96127613	Eya1_peak_1612	84	.	7.61805	13.07283	8.45909	61
chr12	54738493	54738566	Eya1_peak_902	84	.	7.61805	13.07283	8.45909	59
chr11	97187537	97187867	Eya1_peak_731	84	.	7.61805	13.07283	8.45909	295
chr11	69996994	69997077	Eya1_peak_601	84	.	7.61805	13.07283	8.45909	64
chr7	121034528	121035015	Eya1_peak_3597	84	.	7.89251	13.05065	8.44125	427
chr16	13667999	13668095	Eya1_peak_1516	84	.	7.89251	13.05065	8.44125	56
chr2	93900115	93900248	Eya1_peak_2231	84	.	7.59410	13.03491	8.42681	69
chr2	121413993	121414351	Eya1_peak_2271	84	.	7.59410	13.03491	8.42681	251
chr19	45998456	45998553	Eya1_peak_2045	84	.	7.59410	13.03491	8.42681	40
chr16	94570305	94570511	Eya1_peak_1604	84	.	7.59410	13.03491	8.42681	103
chr13	94789039	94789148	Eya1_peak_1166	84	.	7.59410	13.03491	8.42681	67
chr10	7681141	7681697	Eya1_peak_226	84	.	7.59410	13.03491	8.42681	245
chr7	70359126	70359261	Eya1_peak_3513	84	.	7.86530	13.00806	8.40142	36
chr2	18064193	18064394	Eya1_peak_2078	84	.	7.86530	13.00806	8.40142	150
chr5	99978190	99978467	Eya1_peak_3001	83	.	7.57029	12.99721	8.39123	109
chr11	102318702	102318920	Eya1_peak_767	83	.	7.26185	12.96045	8.35585	150
chr8	89042102	89042228	Eya1_peak_3798	83	.	7.54663	12.95974	8.35519	37
chr11	96004659	96004998	Eya1_peak_722	83	.	7.54663	12.95974	8.35519	251
chr15	79690983	79691142	Eya1_peak_1421	83	.	7.52312	12.92249	8.31941	113
chr2	102400624	102400913	Eya1_peak_2238	82	.	7.49976	12.88545	8.28395	102
chr11	54866479	54866893	Eya1_peak_544	82	.	7.49976	12.88545	8.28395	162
chr11	120572573	120572682	Eya1_peak_849	82	.	7.49976	12.88545	8.28395	54
chr3	96172578	96172846	Eya1_peak_2517	82	.	7.78476	12.88204	8.28108	13
chr2	65619924	65620011	Eya1_peak_2180	82	.	7.78476	12.88204	8.28108	37
chr12	100268159	100268239	Eya1_peak_987	82	.	6.93254	12.87234	8.27220	54
chr4	46451360	46451477	Eya1_peak_2655	82	.	7.47654	12.84863	8.24920	83
chr17	33972751	33972903	Eya1_peak_1695	82	.	7.47654	12.84863	8.24920	84
sort: write failed: 'standard output': Broken pipe
sort: write error
In [17]:
cat Eya1_peaks.narrowPeak | wc -l
4164
In [33]:
cat Eya1_peaks.narrowPeak | sort -k9 -g -r | head -1000 > Eya1.chipseq_top1000.narrowpeak
sort: write failed: 'standard output': Broken pipe
sort: write error
In [37]:
cat Eya1.chipseq_top1000.narrowpeak | wc -l
1000
In [40]:
cat Eya1.chipseq_top1000.narrowpeak | head -5
chr9	21950193	21950730	Eya1_peak_3907	1617	.	50.25843	171.22057	161.78474	344
chr15	72568544	72568871	Eya1_peak_1391	1436	.	42.95110	151.40498	143.65936	191
chr13	54970758	54971192	Eya1_peak_1104	1322	.	42.12254	139.63551	132.26416	294
chr12	42972811	42973228	Eya1_peak_893	1307	.	29.34931	138.06731	130.72491	148
chr2	34090652	34090884	Eya1_peak_2140	1264	.	40.58866	133.59843	126.41547	114
cat: write error: Broken pipe

Open the Eya1_peaks.narrowPeak file in IGV. The called peak in the REST.

image.png

Genome-wide ChIP-seq peaks

In [25]:
cat Eya1_peaks.narrowPeak | head
chr1	3670709	3670908	Eya1_peak_1	107	.	8.87783	15.54125	10.72335	128
chr1	4857782	4858014	Eya1_peak_2	108	.	8.35876	15.70195	10.87493	130
chr1	4858153	4858226	Eya1_peak_3	28	.	4.57189	6.68330	2.80234	64
chr1	5022813	5022938	Eya1_peak_4	94	.	7.18023	14.21410	9.49742	59
chr1	8123236	8123343	Eya1_peak_5	207	.	12.61147	26.03038	20.74978	55
chr1	9943673	9943778	Eya1_peak_6	33	.	5.17786	7.29091	3.32999	67
chr1	10037746	10037896	Eya1_peak_7	51	.	6.36931	9.45234	5.19167	33
chr1	10232651	10232724	Eya1_peak_8	33	.	5.42408	7.32244	3.35586	44
chr1	10232850	10233015	Eya1_peak_9	42	.	5.93520	8.42761	4.29727	31
chr1	13373303	13373399	Eya1_peak_10	35	.	5.59359	7.57307	3.56114	24
cat: write error: Broken pipe
In [26]:
cat Eya1_peaks.narrowPeak | cut -f 1-3 > Eya1_peaks.bed
In [27]:
head Eya1_peaks.bed
chr1	3670709	3670908
chr1	4857782	4858014
chr1	4858153	4858226
chr1	5022813	5022938
chr1	8123236	8123343
chr1	9943673	9943778
chr1	10037746	10037896
chr1	10232651	10232724
chr1	10232850	10233015
chr1	13373303	13373399
In [42]:
computeMatrix reference-point \
    -S ChIP_Eya1.bw \
    -R Eya1_peaks.bed \
    --referencePoint center \
    -a 1000 \
    -b 1000 \
    --binSize 5 \
    -out Eya1.tab.gz
#-S: input file
#-R: reference file
#-a -b: choose how broad: each side of the centered of my file
#      If this is full=> enlarge
#binSize 5: take every 5 nucleotides calculated the avg of my bigwig of the sum fit in the matrix
In [43]:
plotHeatmap \
    -m Eya1.tab.gz \
    -out Eya1_peaks.png \
    --heatmapHeight 15  \
    --refPointLabel peak.center \
    --regionsLabel peaks \
    --plotTitle 'ChIP-seq signal'

heatmap show peaks distribution within 2kb around the TSS

There is a big difference in the peak height among the all peaks

Eya1_peaks.png

Motif Analysis

De novo motif discovery

Fetch FASTA sequences of the peaks from UCSC. Upload "Eya1_peaks.narrowPeak" file

image.png

Run RSAT peak-motifs

image.png

image.png

The most significant motif is REST DNA-binding motif(same result as paper) image.png

REST DNA-binding motif belongs to zinc-finger.\ https://www.uniprot.org/uniprotkb/Q8VIG1/entry

REST Uniport image.png

Eya1 don't have DNA binding activity. => Eya1 direct or indirect interacting with REST forming protein complexes bind at REST recognition sequences\ https://www.uniprot.org/uniprotkb/P97767/entry image.png

Eya1 Uniprot image.png

Create a BED file with only the DIRECT peaks = peaks with the REST motif

In [46]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | head
mm10_chr1_3670710_3670908_+	site	dyads_m2dyads_m2	D	16	37	GAGCTGTCCTCGGTGCTGAAAT	19.4
mm10_chr1_5022814_5022938_+	site	dyads_m2dyads_m2	D	31	52	GCACTCTCCAGGGTCCTGACGG	12.6
mm10_chr1_8123237_8123343_+	site	dyads_m2dyads_m2	D	19	40	CCATTGACGCTGGTGCTGAAAT	9.2
mm10_chr1_34579663_34579736_+	site	dyads_m2dyads_m2	D	-24	-3	GAGCTGGCCGTGGTGCTGACGC	16.6
mm10_chr1_35017601_35017692_+	site	dyads_m2dyads_m2	R	15	36	TCGCTGTCCGGGGTACTGATTT	16.4
mm10_chr1_37218520_37218691_+	site	dyads_m2dyads_m2	D	-36	-15	CCGCAGCCCACGGTGCTGAAAC	11.0
mm10_chr1_38939742_38939850_+	site	dyads_m2dyads_m2	D	-12	9	ACGCTGTCCACGGTGCTGACCG	17.9
mm10_chr1_56839045_56839203_+	site	dyads_m2dyads_m2	D	-36	-15	GTCCTGTCCATGGTACTGAAAT	20.7
mm10_chr1_63614753_63614856_+	site	dyads_m2dyads_m2	R	-8	13	GTGCTGTCCGGGGTGCTGAAGT	18.8
mm10_chr1_64158927_64159059_+	site	dyads_m2dyads_m2	R	-49	-28	GCTCTGTCCATGGTCCTGACTC	18.3
grep: write error: Broken pipe
In [47]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | cut -f 1 | tr "_" "\t" | cut -f 2-4 | head
chr1	3670710	3670908
chr1	5022814	5022938
chr1	8123237	8123343
chr1	34579663	34579736
chr1	35017601	35017692
chr1	37218520	37218691
chr1	38939742	38939850
chr1	56839045	56839203
chr1	63614753	63614856
chr1	64158927	64159059
cut: write error: Broken pipe
In [48]:
cat peak-motifs_dyads_m2dyads_m2_sites.tab | grep -v ";" | grep -v '#' | cut -f 1 | tr "_" "\t" | cut -f 2-4 > Eya1_peaks-with-motif-RSAT.bed
In [50]:
cat Eya1_peaks-with-motif-RSAT.bed
chr1	3670710	3670908
chr1	5022814	5022938
chr1	8123237	8123343
chr1	34579663	34579736
chr1	35017601	35017692
chr1	37218520	37218691
chr1	38939742	38939850
chr1	56839045	56839203
chr1	63614753	63614856
chr1	64158927	64159059
chr1	70725722	70725836
chr1	72537069	72537240
chr1	74858138	74858319
chr1	74891633	74891795
chr1	75263097	75263292
chr1	75277344	75277424
chr1	84696319	84696436
chr1	90028489	90028604
chr1	90028489	90028604
chr1	90028489	90028604
chr1	90028489	90028604
chr1	93272617	93272762
chr1	99772343	99772459
chr1	120331986	120332093
chr1	120390483	120390592
chr1	127496888	127497019
chr1	134664962	134665103
chr1	152956323	152956491
chr1	155594281	155594376
chr1	158019287	158019398
chr1	159524228	159524358
chr1	159621427	159621554
chr1	159702167	159702307
chr1	167079656	167079740
chr1	167123707	167123798
chr1	167187922	167188027
chr1	173361729	173361968
chr1	173361729	173361968
chr1	176697238	176697317
chr1	192457672	192457793
chr1	192472443	192472628
chr1	193036044	193036249
chr1	193738991	193739063
chr10	5639266	5639357
chr10	6788820	6788922
chr10	11081595	11081712
chr10	39967695	39967810
chr10	40961494	40961625
chr10	41071876	41071989
chr10	45483377	45483462
chr10	45546998	45547078
chr10	60914532	60914664
chr10	62138164	62138285
chr10	70598412	70598511
chr10	71403718	71403833
chr10	71428394	71428502
chr10	76958349	76958430
chr10	76978198	76978287
chr10	79718076	79718250
chr10	80748722	80748926
chr10	81477669	81477831
chr10	89224655	89224792
chr10	90376747	90376830
chr10	90823555	90823711
chr10	90827074	90827171
chr10	90881001	90881087
chr10	94305645	94305759
chr10	110676638	110676790
chr10	116019305	116019426
chr10	119705488	119705586
chr10	126625614	126625701
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr10	126681029	126681354
chr11	3153742	3153926
chr11	3774705	3774885
chr11	4076791	4076896
chr11	4750372	4750579
chr11	4763733	4763837
chr11	4949327	4949562
chr11	6016491	6016608
chr11	33680217	33680365
chr11	33787450	33787628
chr11	34448046	34448189
chr11	35798960	35799121
chr11	35798960	35799121
chr11	36090293	36090410
chr11	36396433	36396567
chr11	41999617	41999713
chr11	48012993	48013098
chr11	48696466	48696591
chr11	54303183	54303314
chr11	54343856	54343982
chr11	55607774	55608073
chr11	55897638	55897811
chr11	56812249	56812393
chr11	57434299	57434411
chr11	66259010	66259091
chr11	71389716	71389801
chr11	71937241	71937369
chr11	72113451	72113552
chr11	72494158	72494244
chr11	72607941	72608230
chr11	74619245	74619433
chr11	75173489	75173618
chr11	77930845	77931116
chr11	78496010	78496134
chr11	78952633	78952713
chr11	79593696	79593768
chr11	80312747	80312819
chr11	81005976	81006074
chr11	81115801	81115945
chr11	81194030	81194109
chr11	81966911	81966984
chr11	82313251	82313387
chr11	82371713	82371850
chr11	82514891	82515002
chr11	83417207	83417312
chr11	83421429	83421554
chr11	84662129	84662247
chr11	84724270	84724380
chr11	84729359	84729474
chr11	87921111	87921238
chr11	87957133	87957328
chr11	88047786	88048289
chr11	93097151	93097230
chr11	97078907	97079000
chr11	98314192	98314325
chr11	98324123	98324254
chr11	100203590	100203746
chr11	100758920	100759198
chr11	101602625	101602774
chr11	102393331	102393560
chr11	103656674	103656822
chr11	103920709	103921013
chr11	103920709	103921013
chr11	104053377	104053512
chr11	104114854	104114970
chr11	104198020	104198141
chr11	107817341	107817443
chr11	114652620	114652754
chr11	115052278	115052540
chr11	115052278	115052540
chr11	116920917	116921006
chr11	117873060	117873259
chr11	118584818	118585200
chr11	118584818	118585200
chr11	118584818	118585200
chr11	118584818	118585200
chr11	118603279	118603390
chr11	118659411	118659517
chr12	3955551	3955646
chr12	5111488	5111569
chr12	5717648	5717738
chr12	8099976	8100084
chr12	28831171	28831271
chr12	29465327	29465463
chr12	33084806	33084926
chr12	47252478	47252556
chr12	52504253	52504671
chr12	70347181	70347333
chr12	72422823	72422913
chr12	81206309	81206435
chr12	81776303	81776375
chr12	84698612	84698781
chr12	86547928	86548050
chr12	86983590	86983730
chr12	86994361	86994448
chr12	88709455	88709575
chr12	92040611	92040719
chr12	99041727	99041844
chr12	100268160	100268239
chr12	102550608	102550779
chr12	102555086	102555314
chr12	102949729	102949830
chr12	105266242	105266380
chr12	105266242	105266380
chr12	105322218	105322521
chr12	105322218	105322521
chr12	105322218	105322521
chr12	105322218	105322521
chr12	106115159	106115318
chr12	106633219	106633338
chr12	107464874	107464974
chr12	108994781	108994927
chr12	112141407	112141544
chr12	112511239	112511343
chr12	113188124	113188230
chr13	22035883	22036035
chr13	23990957	23991111
chr13	25269143	25269418
chr13	42447111	42447197
chr13	42711669	42711814
chr13	46097094	46097222
chr13	53948188	53948311
chr13	54260413	54260488
chr13	54371707	54371805
chr13	54749475	54749613
chr13	54750798	54751180
chr13	54750798	54751180
chr13	54758488	54758573
chr13	54876696	54876781
chr13	54945434	54945584
chr13	54970759	54971192
chr13	56895534	56895658
chr13	57867715	57867791
chr13	58663436	58663596
chr13	69896674	69896746
chr13	72902707	72902799
chr13	94878449	94878525
chr13	99564494	99564605
chr13	99900548	99900724
chr13	100210559	100210856
chr13	100210559	100210856
chr13	105442715	105442844
chr13	107419488	107419610
chr13	117604260	117604358
chr14	12530303	12530440
chr14	12823964	12824038
chr14	16365377	16365978
chr14	20093659	20093738
chr14	29657149	29657299
chr14	32321745	32322035
chr14	32597331	32597466
chr14	34867425	34867526
chr14	37016043	37016212
chr14	37068650	37068846
chr14	51985310	51985466
chr14	63681556	63681840
chr14	63681556	63681840
chr14	63681556	63681840
chr14	63713050	63713362
chr14	63713050	63713362
chr14	63713050	63713362
chr14	64568661	64568878
chr14	66161494	66161584
chr14	66909854	66909969
chr14	68125672	68125796
chr14	75366894	75367015
chr14	77195461	77195546
chr14	79769759	79769951
chr14	79785518	79785639
chr14	80157118	80157246
chr14	80215913	80216097
chr14	80257220	80257330
chr14	103536519	103536593
chr14	104453992	104454087
chr14	108913802	108914035
chr15	25118126	25118232
chr15	26309752	26309933
chr15	27655141	27655234
chr15	28823680	28823819
chr15	30913495	30913595
chr15	72201012	72201104
chr15	72568545	72568871
chr15	72568545	72568871
chr15	72568545	72568871
chr15	72568545	72568871
chr15	72689745	72690132
chr15	73026827	73027022
chr15	74076017	74076321
chr15	74076017	74076321
chr15	74382669	74382810
chr15	74549584	74549683
chr15	76521888	76522503
chr15	76521888	76522503
chr15	76722326	76722450
chr15	78066633	78066758
chr15	78119784	78120090
chr15	78119784	78120090
chr15	78153249	78153321
chr15	79791636	79791834
chr15	80203515	80203647
chr15	80277768	80277892
chr15	82921206	82921352
chr15	83879985	83880068
chr15	83924821	83924920
chr15	84086473	84086599
chr15	84109067	84109254
chr15	84829445	84829795
chr15	84829445	84829795
chr15	84829445	84829795
chr15	84965683	84965843
chr15	86544203	86544369
chr15	86932808	86932930
chr15	87887165	87887242
chr15	88325296	88325368
chr15	89150197	89150315
chr15	96460651	96460796
chr15	101473073	101473202
chr15	101879893	101880025
chr16	5765283	5765409
chr16	8914355	8914447
chr16	9836670	9836762
chr16	10501955	10502129
chr16	12359233	12359356
chr16	23890282	23890385
chr16	23890282	23890385
chr16	34400466	34400607
chr16	35302507	35303112
chr16	35302507	35303112
chr16	39985142	39985250
chr16	62758480	62758601
chr16	62758480	62758601
chr16	89071187	89071259
chr16	91011567	91011667
chr16	94972576	94972698
chr16	97286890	97286989
chr17	6256457	6256643
chr17	6321825	6322006
chr17	6490668	6490839
chr17	7741125	7741260
chr17	9066781	9066892
chr17	11309999	11310100
chr17	25239678	25239883
chr17	25400557	25400717
chr17	25813615	25813805
chr17	25813615	25813805
chr17	27228669	27228818
chr17	27466781	27466908
chr17	28575545	28575734
chr17	29362151	29362243
chr17	30938814	30938892
chr17	33972752	33972903
chr17	33972752	33972903
chr17	35270105	35270255
chr17	46704615	46704743
chr17	65370188	65370305
chr17	69439315	69439460
chr17	69969144	69969247
chr17	72603210	72603409
chr17	73488012	73488159
chr17	74489616	74489750
chr17	83010983	83011137
chr17	83010983	83011137
chr17	84820740	84820865
chr17	87798526	87798678
chr17	91092802	91092976
chr18	20916236	20916364
chr18	25500580	25500731
chr18	25668105	25668408
chr18	25668105	25668408
chr18	25668105	25668408
chr18	25668105	25668408
chr18	25668105	25668408
chr18	25752877	25753035
chr18	31447124	31447263
chr18	31760171	31760350
chr18	35977608	35977731
chr18	36004726	36004901
chr18	38056481	38056573
chr18	38075458	38075672
chr18	42396151	42396368
chr18	63977173	63977328
chr18	64042670	64042829
chr18	64266566	64266682
chr18	66561052	66561213
chr18	70411116	70411244
chr18	74608258	74608333
chr18	77274358	77274452
chr18	77417641	77417764
chr18	82030207	82030311
chr19	4988971	4989348
chr19	4988971	4989348
chr19	4988971	4989348
chr19	4988971	4989348
chr19	4992514	4992661
chr19	6502709	6502895
chr19	10403191	10403441
chr19	10403191	10403441
chr19	22139294	22139436
chr19	28818398	28818542
chr19	30030697	30030894
chr19	35833125	35833289
chr19	38558973	38559076
chr19	41661112	41661246
chr19	42255858	42256209
chr19	42255858	42256209
chr19	42255858	42256209
chr19	42326041	42326167
chr19	42425337	42425481
chr19	42636762	42636890
chr19	44692486	44692627
chr19	45097978	45098097
chr19	45813859	45814038
chr19	47006444	47006633
chr19	47016609	47016760
chr19	48168454	48168548
chr19	60469021	60469130
chr2	19429102	19429235
chr2	24488797	24488869
chr2	24762019	24762151
chr2	25318879	25319146
chr2	26208195	26208359
chr2	27142535	27142630
chr2	28195125	28195226
chr2	28916127	28916366
chr2	28916127	28916366
chr2	29310113	29310204
chr2	29573697	29573853
chr2	31346213	31346375
chr2	33018084	33018377
chr2	33018084	33018377
chr2	34090653	34090884
chr2	34090653	34090884
chr2	38418041	38418332
chr2	38418041	38418332
chr2	43613686	43613824
chr2	49503772	49503852
chr2	65619925	65620011
chr2	70559665	70559781
chr2	79454294	79454427
chr2	91921279	91921406
chr2	92401272	92401451
chr2	92671845	92671931
chr2	93071777	93071900
chr2	93900116	93900248
chr2	94524684	94524781
chr2	104299333	104299426
chr2	109675986	109676095
chr2	109675986	109676095
chr2	125135863	125136059
chr2	129715790	129715958
chr2	132781745	132781971
chr2	136714190	136714441
chr2	136714190	136714441
chr2	143207327	143207442
chr2	143536639	143536733
chr2	143546890	143547023
chr2	146226686	146226805
chr2	153032234	153032552
chr2	153032234	153032552
chr2	154076392	154076499
chr2	155775684	155775849
chr2	156652958	156653099
chr2	156677011	156677161
chr2	156677011	156677161
chr2	157663727	157663873
chr2	157913187	157913670
chr2	157913187	157913670
chr2	157913187	157913670
chr2	157913187	157913670
chr2	157970789	157970940
chr2	158570516	158570602
chr2	158584724	158584892
chr2	162031749	162031852
chr2	162568861	162568951
chr2	163439325	163439404
chr2	163564808	163564883
chr2	163889529	163889648
chr2	164966519	164966693
chr2	164968565	164968847
chr2	164979887	164979984
chr2	165159193	165159287
chr2	165160595	165160713
chr2	165456855	165456944
chr2	172042194	172042371
chr2	172110847	172110963
chr2	172320989	172321167
chr2	178277339	178277447
chr2	178330167	178330283
chr2	178735198	178735363
chr2	179193799	179193992
chr2	179193799	179193992
chr2	179193799	179193992
chr2	179616048	179616178
chr2	180104446	180104659
chr2	180417827	180417975
chr2	180756016	180756195
chr2	180894493	180894587
chr2	181126252	181126325
chr2	181302111	181302304
chr2	181302111	181302304
chr3	8508197	8508289
chr3	19694585	19694718
chr3	27370243	27370442
chr3	31309005	31309146
chr3	68064923	68065004
chr3	80802945	80803070
chr3	82412563	82412651
chr3	87993580	87993708
chr3	88220951	88221124
chr3	89159264	89159459
chr3	89764408	89764587
chr3	91213401	91213576
chr3	99311031	99311115
chr3	103573909	103574051
chr3	105275376	105275513
chr3	105577888	105577960
chr3	105959121	105959208
chr3	106962642	106962724
chr3	114904086	114904296
chr3	118431460	118431649
chr3	123508056	123508277
chr3	141811524	141811654
chr3	152821319	152821453
chr3	153267556	153267657
chr3	154819851	154819959
chr4	14145577	14145715
chr4	21712176	21712488
chr4	32601240	32601381
chr4	41532576	41532679
chr4	41546059	41546187
chr4	41606936	41607028
chr4	42945215	42945303
chr4	44260460	44260599
chr4	44434731	44434828
chr4	44511812	44511959
chr4	44578713	44578854
chr4	46992962	46993103
chr4	62257085	62257219
chr4	68955763	68955896
chr4	87221698	87221826
chr4	88722072	88722269
chr4	89313630	89313752
chr4	91379642	91379731
chr4	101550801	101550881
chr4	103572054	103572216
chr4	103875699	103875848
chr4	110119538	110119653
chr4	115728848	115728989
chr4	115887034	115887108
chr4	117893530	117893660
chr4	120866403	120866559
chr4	120880860	120880952
chr4	124317180	124317369
chr4	124633417	124633556
chr4	124882441	124882530
chr4	125300596	125300847
chr4	125300596	125300847
chr4	125300596	125300847
chr4	125328941	125329079
chr4	125503020	125503098
chr4	125590608	125590770
chr4	125835364	125835501
chr4	126655448	126655657
chr4	126655448	126655657
chr4	127173607	127173795
chr4	127173607	127173795
chr4	127619950	127620180
chr4	127619950	127620180
chr4	127619950	127620180
chr4	127970280	127970407
chr4	128042768	128042895
chr4	128248844	128248957
chr4	128913953	128914066
chr4	129120918	129121245
chr4	131115342	131115587
chr4	131115342	131115587
chr4	131658047	131658174
chr4	134020694	134020964
chr4	134020694	134020964
chr4	136907187	136907333
chr4	136924580	136924844
chr4	136924580	136924844
chr4	137676186	137676333
chr4	138597876	138598053
chr4	139059695	139059859
chr4	140258966	140259346
chr4	140258966	140259346
chr4	140258966	140259346
chr4	140258966	140259346
chr4	140258966	140259346
chr4	140283502	140283714
chr4	140283502	140283714
chr4	140283502	140283714
chr4	140358225	140358382
chr4	147957271	147957376
chr4	148229756	148229958
chr4	148229756	148229958
chr4	148286817	148286918
chr4	148293340	148293553
chr4	151185896	151185986
chr4	151186525	151186729
chr4	151288931	151289470
chr4	151288931	151289470
chr4	151288931	151289470
chr4	151288931	151289470
chr4	151288931	151289470
chr4	151288931	151289470
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151604518	151605412
chr4	151759272	151759375
chr4	152287047	152287180
chr4	152424500	152424609
chr4	153189630	153189775
chr4	153357660	153357770
chr4	153679298	153679421
chr4	154466462	154466552
chr4	155018792	155018938
chr4	155397641	155397757
chr4	155859356	155859714
chr4	155859356	155859714
chr4	155859356	155859714
chr4	155859356	155859714
chr5	22236949	22237074
chr5	24357560	24357689
chr5	26535697	26535783
chr5	26894492	26894592
chr5	27052588	27052660
chr5	27366083	27366208
chr5	27737223	27737424
chr5	31815285	31815357
chr5	33438279	33438516
chr5	33438279	33438516
chr5	35531808	35531898
chr5	36836091	36836213
chr5	36896317	36896416
chr5	37009890	37010211
chr5	37009890	37010211
chr5	37009890	37010211
chr5	37009890	37010211
chr5	37131994	37132077
chr5	37243472	37243665
chr5	37257374	37257507
chr5	37557633	37557710
chr5	62483690	62483780
chr5	63689228	63689318
chr5	77265819	77266303
chr5	99707419	99707500
chr5	110558515	110558623
chr5	111901766	111901956
chr5	111987170	111987246
chr5	112718669	112718984
chr5	112718669	112718984
chr5	113292306	113292399
chr5	113407465	113407592
chr5	113564620	113564746
chr5	113716719	113716909
chr5	115946110	115946187
chr5	116154995	116155122
chr5	116518203	116518286
chr5	116545914	116546006
chr5	116554042	116554146
chr5	116591455	116591613
chr5	116714392	116714511
chr5	116829932	116830089
chr5	116829932	116830089
chr5	116914997	116915148
chr5	117264876	117264980
chr5	117844737	117844876
chr5	120424129	120424289
chr5	121009543	121009704
chr5	121068819	121068935
chr5	121926531	121926676
chr5	124148454	124148536
chr5	127192015	127192132
chr5	128348959	128349062
chr5	128879280	128879376
chr5	129287600	129287710
chr5	130363921	130364012
chr5	135742280	135742352
chr5	135843520	135843678
chr5	137030209	137030384
chr5	137031178	137031280
chr5	137031178	137031280
chr5	137135130	137135220
chr5	139979035	139979141
chr5	140218059	140218151
chr5	141985169	141985312
chr5	142694733	142694862
chr5	144491403	144491686
chr5	144491403	144491686
chr5	146360503	146360631
chr5	146644639	146644821
chr5	148071931	148072110
chr6	8948577	8948727
chr6	8957615	8957735
chr6	28982517	28982671
chr6	31307166	31307298
chr6	31717640	31717761
chr6	31883868	31883992
chr6	31885340	31885456
chr6	31885340	31885456
chr6	32710304	32710467
chr6	36378093	36378170
chr6	45059215	45059366
chr6	48137004	48137102
chr6	52713755	52714160
chr6	55108442	55108645
chr6	83927573	83927689
chr6	84365133	84365205
chr6	84674281	84674353
chr6	85498318	85498404
chr6	89070122	89070258
chr6	95223627	95223782
chr6	113193843	113194095
chr6	113282090	113282216
chr6	113843378	113843450
chr6	113852456	113852686
chr6	113881920	113882081
chr6	114087247	114087392
chr6	115178978	115179091
chr6	118001456	118001560
chr6	119233175	119233286
chr6	119320632	119320747
chr6	121473010	121473450
chr6	121473010	121473450
chr6	122659692	122659843
chr6	127767905	127768115
chr6	128469529	128469648
chr6	139010656	139010728
chr6	146437008	146437147
chr7	4178528	4178727
chr7	4178528	4178727
chr7	4830660	4830860
chr7	6410076	6410420
chr7	6410076	6410420
chr7	6410076	6410420
chr7	6410076	6410420
chr7	16147766	16147930
chr7	16183793	16183984
chr7	18951535	18951660
chr7	19573201	19573338
chr7	24359378	24359579
chr7	24359378	24359579
chr7	24727774	24727900
chr7	25146040	25146178
chr7	27396258	27396331
chr7	28263919	28264083
chr7	28505736	28505819
chr7	30346762	30346943
chr7	30434363	30434457
chr7	30484369	30484466
chr7	34702895	34703009
chr7	39455939	39456083
chr7	40762728	40762818
chr7	44335741	44335866
chr7	44593894	44594090
chr7	44770096	44770391
chr7	44770096	44770391
chr7	44770096	44770391
chr7	49910556	49910667
chr7	51621838	51621946
chr7	57592313	57592438
chr7	70360030	70360230
chr7	81493355	81493552
chr7	82625452	82625609
chr7	82625452	82625609
chr7	84085101	84085250
chr7	99648812	99648944
chr7	101438008	101438111
chr7	109129582	109129672
chr7	110701764	110701977
chr7	111081803	111082617
chr7	117021828	117021986
chr7	117636815	117636933
chr7	117636815	117636933
chr7	118001238	118001389
chr7	119111922	119112020
chr7	119356363	119356475
chr7	120426819	120426891
chr7	121391351	121391471
chr7	121596534	121596651
chr7	121730340	121730494
chr7	122670869	122671111
chr7	122670869	122671111
chr7	123235572	123235699
chr7	123503470	123503594
chr7	124199058	124199195
chr7	124742214	124742340
chr7	124989615	124989700
chr7	126825590	126825694
chr7	128231876	128231995
chr7	129469620	129469785
chr7	131245159	131245277
chr7	131917501	131917602
chr7	132060260	132060385
chr7	133511085	133511178
chr7	137945135	137945253
chr7	138084023	138084287
chr7	138084023	138084287
chr7	138084023	138084287
chr7	138084023	138084287
chr7	138084023	138084287
chr7	141973455	141973557
chr7	144160232	144160310
chr7	144294419	144294512
chr8	9309609	9309725
chr8	9635325	9635499
chr8	9635325	9635499
chr8	9769204	9769332
chr8	14072572	14072895
chr8	14072572	14072895
chr8	14072572	14072895
chr8	14072572	14072895
chr8	38747310	38747394
chr8	55754335	55754418
chr8	55940689	55940811
chr8	70885757	70885878
chr8	71483977	71484105
chr8	74851958	74852038
chr8	78431493	78431646
chr8	78438371	78438447
chr8	84454689	84454862
chr8	84471317	84471557
chr8	84947107	84947546
chr8	84947107	84947546
chr8	87087611	87087685
chr8	87700496	87700606
chr8	94482282	94482380
chr8	94800800	94800914
chr8	95028538	95028634
chr8	105291038	105291153
chr8	105693811	105693911
chr8	110196825	110196940
chr8	112128885	112129121
chr8	112128885	112129121
chr8	112404221	112404340
chr8	117173845	117173919
chr8	118951924	118951996
chr8	119164208	119164292
chr8	119258690	119258895
chr8	119258690	119258895
chr8	119258690	119258895
chr8	121736356	121736468
chr8	121761638	121761747
chr8	123414388	123414507
chr8	123891459	123891548
chr8	126404663	126404774
chr9	20813142	20813267
chr9	20857161	20857410
chr9	20857161	20857410
chr9	21950194	21950730
chr9	21950194	21950730
chr9	22053846	22053918
chr9	26727584	26727693
chr9	27308179	27308324
chr9	29146083	29146171
chr9	34837837	34837965
chr9	40269712	40269789
chr9	40801359	40801567
chr9	40873797	40873996
chr9	42652863	42652959
chr9	43698590	43698715
chr9	43934766	43934893
chr9	43959625	43959808
chr9	45710578	45710656
chr9	46642809	46642992
chr9	48898725	48898797
chr9	49341153	49341294
chr9	50029218	50029290
chr9	54271040	54271153
chr9	55026329	55026440
chr9	56738430	56738534
chr9	57468142	57468242
chr9	58060893	58061158
chr9	58841787	58841938
chr9	59578344	59578528
chr9	61484519	61484641
chr9	64624677	64624805
chr9	64666647	64666840
chr9	69856757	69856876
chr9	74868518	74868626
chr9	89737423	89737518
chr9	98234884	98234980
chr9	99218354	99218632
chr9	99563876	99564020
chr9	100023788	100023888
chr9	104569428	104569631
chr9	105272452	105272524
chr9	105893820	105893905
chr9	107381813	107381945
chr9	108825914	108825992
chr9	108826580	108827252
chr9	119149702	119149869
chr9	119389102	119389237
chr9	119706828	119706971
chr9	121791343	121791495
chr9	122006690	122006819
chrUn	JH584304	4617
chrX	7795194	7795274
chrX	73869426	73869643
chrX	73869426	73869643
chrX	143904847	143904930

Position-Specific Scoring Matrix (PSSM) and track enrichment

Peaks correlate with other epigenomic data sets called tracks.\ i-cisTarget will test for enrichment of motifs, using a collection of databases of PSSMs, as well as tracks.\ Position-Specific Scoring Matrix = position weight matrix (PWM)

image.png

results: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget/reports/41dd79b45c7da1b642ac42b0659d97a0eb6641e9/report.html

The most significantly motif was the REST (same result as RSAT database and paper)\ REST => transcriptional repressor that represses neuronal genes in non-neuronal tissues. It also found in undifferentiated neuronal progenitor cells. image.png

Leading edge in i-cisTarget for the REST motif = directly bound regions

In [59]:
cat hocomoco__REST_MOUSE.H11MO.0.A.targets.bed | head
track name=hocomoco__REST_MOUSE.H11MO.0.A_candidate_targets description="" useScore=1
chr8	84454553	84454901	chr8:84454553-84454901
chr4	125328868	125329138	chr4:125328868-125329138
chr8	86425479	86425678	chr8:86425479-86425678
chrX	7795139	7795303	chrX:7795139-7795303
chr16	89071105	89071366	chr16:89071105-89071366
chr14	79785452	79785717	chr14:79785452-79785717
chr6	146437016	146437257	chr6:146437016-146437257
chr17	83010904	83011155	chr17:83010904-83011155
chr14	80157069	80157323	chr14:80157069-80157323
In [60]:
cat hocomoco__REST_MOUSE.H11MO.0.A.targets.bed  | wc -l
672

672 peaks are in the leading edge, and the total peaks of Eya1 is 4164.\ Therefore, 16% of the input peaks contain a good match of the REST motif.

http://great.stanford.edu/public/html/

  1. with all Eyal1 peaks

image.png

The Eya1 peaks is associated with transcriptional, posttranscriptional, translational regulation and histone modification. image.png

  1. peaks with REST motif (Eya1_peaks-with-motif-RSAT.bed file)

image.png

The Eya1 peaks occupied in REST motif is related to synaptic transmission, ion transport and secretion. image.png

  1. peaks with REST motif (Eya1_peaks-with-motif-iCisTarget.bed file)

The result is almost the same as the result of REST motif in RSAT database. image.png

Using STRING to identify which gene are ssociated with REST.

image.png

In [26]:
cat string_protein_annotations_REST.tsv | cut -f1 | head
#node
Actl6a
Actl6b
Arid4a
Arid4b
Batf
Bdnf
Bptf
Brms1
Btrc
In [27]:
cat string_protein_annotations_REST.tsv | cut -f 1 | grep -v '#' > REST-string-top100.txt
In [15]:
list=`cat REST-string-top100.txt`

Next step, find the common genes shown both in REST motif (Eya1_peaks-with-motif-RSAT) and REST in SRING database (REST-string-top100.txt).

image.png

In [16]:
for i in $list; do grep -w $i 1GREAT_REST_targets_regulation_of_membrane_potential.txt; done
unnamed	Bdnf (+1341)
unnamed	Bdnf (+1341)

In [13]:
for i in $list; do grep -w $i 2GREAT_REST_modulation_of_synaptic_transmission.txt; done
unnamed	Bdnf (+1341)
unnamed	Bdnf (+1341)
unnamed	Creb1 (-373816)

In [17]:
for i in $list; do grep -w $i 3GREAT_REST_targets_neuromuscular_process_controlling_balance.txt; done

In [18]:
for i in $list; do grep -w $i 4GREAT_REST_targets_cation_transport.txt; done
unnamed	Rest (+570)

In [19]:
for i in $list; do grep -w $i 5GREAT_REST_targets_trans-synaptic_signaling.txt; done
unnamed	Lin7c (-214812), Bdnf (+1341)
unnamed	Lin7c (-214812), Bdnf (+1341)

In [20]:
for i in $list; do grep -w $i 7GREAT_REST_targets_signal_release.txt; done
unnamed	Neurod1 (+2390)

In [21]:
for i in $list; do grep -w $i 15GREAT_REST_targets_neurotransmitter_transport.txt; done

Few genes found => use 300 number of STRING

In [23]:
cat string_protein_annotations_REST_300.tsv | cut -f1 | head
#node
Actl6a
Actl6b
Ar
Arid4a
Arid4b
Ascl1
Batf
Bdnf
Bptf
In [28]:
cat string_protein_annotations_REST_300.tsv | cut -f 1 | grep -v '#' > REST-string-top300.txt
In [29]:
list=`cat REST-string-top300.txt`
In [30]:
for i in $list; do grep -w $i 1GREAT_REST_targets_regulation_of_membrane_potential.txt; done
unnamed	Bdnf (+1341)
unnamed	Bdnf (+1341)

In [31]:
for i in $list; do grep -w $i 2GREAT_REST_modulation_of_synaptic_transmission.txt; done
unnamed	Bdnf (+1341)
unnamed	Bdnf (+1341)
unnamed	Creb1 (-373816)

In [32]:
for i in $list; do grep -w $i 3GREAT_REST_targets_neuromuscular_process_controlling_balance.txt; done

In [33]:
for i in $list; do grep -w $i 4GREAT_REST_targets_cation_transport.txt; done
unnamed	Rest (+570)

In [34]:
for i in $list; do grep -w $i 5GREAT_REST_targets_trans-synaptic_signaling.txt; done
unnamed	Lin7c (-214812), Bdnf (+1341)
unnamed	Lin7c (-214812), Bdnf (+1341)
unnamed	Nrxn2 (+84071)
unnamed	Nrxn3 (-84989)

In [35]:
for i in $list; do grep -w $i 7GREAT_REST_targets_signal_release.txt; done
unnamed	Neurod1 (+2390)
unnamed	Nrxn2 (+84071)
unnamed	Nrxn3 (-84989)

In [36]:
for i in $list; do grep -w $i 15GREAT_REST_targets_neurotransmitter_transport.txt; done
unnamed	Nrxn2 (+84071)
unnamed	Nrxn3 (-84989)

Only 7 genes shown both in REST-related STRING database and REST-motif GREAT database. \ => these genes are both ChIP-seq peak nearby (<50kb) and somehow associated with REST.

Comparison of STRING and iRegulon

Analze with iRegulon to see the motif and targets are already connected

In [37]:
list=`cat REST-string-top300.txt`
In [38]:
for i in $list; do grep -w $i REST_target_gene_iRegulon_geneID.txt; done
Nr2e1	21907	
Srrm4	68955	

Only 2 genes are found => the target gene of REST are few reported => we can validate these genes whether they are directly bound with REST by implementing experiments to proof.

Nr2e1 => an orphan receptor involved in the regulation of retinal development and essential for vision\ Srrm4 => required for neural cell differentiation.

Conclusion

Two strategy: De novo motif discovery (RSAT peak-motifs) and enrichment of motifs (i-cis Target) both identified recognition site is GCTGTCCATGGTGCTGAA which belongs to REST motif. The result point out that Eya1 does not directly bind to DNA and must through its interacting partners such as REST(zinc-finger transcriptional repressor) or other co-regulator to activate or repress gene expression. The result of finding REST is the same as when utilizing iRegulon of bulk RNA-seq analysis.

GREAT database indicate that Eya1-occupied REST motif peaks are gene about synaptic transmission, ion transport and secretion, all about neuron, but no nephron-related term was enriched. Interestingly, the author also use Six2 Chip analysis and overlap of Eya1 peaks and Six2 peaks. They both identify REST recognition sequences, suggesting that Eya1 cooperate with Six2 through REST transcription factor to regulate gene expression and further maintain the NPSc identity.